Starting phenix.real_space_refine on Thu Jun 12 14:37:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugs_42234/06_2025/8ugs_42234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugs_42234/06_2025/8ugs_42234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ugs_42234/06_2025/8ugs_42234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugs_42234/06_2025/8ugs_42234.map" model { file = "/net/cci-nas-00/data/ceres_data/8ugs_42234/06_2025/8ugs_42234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugs_42234/06_2025/8ugs_42234.cif" } resolution = 3.2 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= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4 5.49 5 Mg 2 5.21 5 S 97 5.16 5 C 8909 2.51 5 N 2351 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13961 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6682 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 31, 'TRANS': 784} Chain: "B" Number of atoms: 6634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6634 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 32, 'TRANS': 783} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 269 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain breaks: 1 Chain: "D" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 280 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 4, 'TRANS': 30} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.33, per 1000 atoms: 0.60 Number of scatterers: 13961 At special positions: 0 Unit cell: (95.63, 125.76, 170.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 97 16.00 P 4 15.00 Mg 2 11.99 O 2596 8.00 N 2351 7.00 C 8909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.19 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 599 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 563 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 597 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 561 " 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 61.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.656A pdb=" N PHE A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 16 " --> pdb=" O PHE A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.627A pdb=" N ALA A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.661A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.761A pdb=" N GLU A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 204 through 250 removed outlier: 4.144A pdb=" N ASN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.037A pdb=" N ASN A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 431 through 459 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.607A pdb=" N ILE A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 removed outlier: 3.983A pdb=" N LYS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 560 through 578 Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.908A pdb=" N ARG A 582 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 625 through 641 removed outlier: 3.602A pdb=" N ASP A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 669 Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.604A pdb=" N TYR A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 691 Processing helix chain 'A' and resid 693 through 704 removed outlier: 3.674A pdb=" N TRP A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 3.768A pdb=" N LEU A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 753 removed outlier: 4.095A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 767 No H-bonds generated for 'chain 'A' and resid 765 through 767' Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 780 through 792 removed outlier: 3.656A pdb=" N VAL A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 821 Processing helix chain 'B' and resid 8 through 15 Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 47 through 68 removed outlier: 3.808A pdb=" N GLU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.738A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.782A pdb=" N GLU B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 213 through 247 Processing helix chain 'B' and resid 252 through 264 Processing helix chain 'B' and resid 264 through 269 removed outlier: 4.373A pdb=" N ASN B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.314A pdb=" N SER B 342 " --> pdb=" O TRP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 360 through 363 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 428 through 457 removed outlier: 3.708A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 481 through 493 Processing helix chain 'B' and resid 512 through 527 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.673A pdb=" N LYS B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 559 through 575 removed outlier: 6.258A pdb=" N VAL B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 removed outlier: 3.958A pdb=" N SER B 580 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'B' and resid 605 through 613 removed outlier: 3.500A pdb=" N GLN B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 621 Processing helix chain 'B' and resid 623 through 639 removed outlier: 3.619A pdb=" N GLU B 639 " --> pdb=" O PHE B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 643 Processing helix chain 'B' and resid 649 through 667 removed outlier: 3.548A pdb=" N THR B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 689 removed outlier: 3.574A pdb=" N LYS B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 700 Processing helix chain 'B' and resid 702 through 719 Processing helix chain 'B' and resid 719 through 724 removed outlier: 4.351A pdb=" N THR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 750 removed outlier: 4.562A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 766 through 778 Processing helix chain 'B' and resid 778 through 790 removed outlier: 3.672A pdb=" N VAL B 782 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 822 Processing helix chain 'D' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.721A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE A 113 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET A 94 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 11.427A pdb=" N ALA A 101 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 14.236A pdb=" N ASP A 187 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASN A 184 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 190 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 333 removed outlier: 4.077A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133 removed outlier: 6.810A pdb=" N LEU B 94 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE B 111 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N CYS B 92 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 113 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP B 90 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 89 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS B 195 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 91 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 187 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N GLN B 99 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 14.321A pdb=" N ASP B 185 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASN B 182 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 188 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 331 removed outlier: 3.986A pdb=" N LYS B 315 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS B 270 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 404 " --> pdb=" O CYS B 270 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 397 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN B 382 " --> pdb=" O ASN B 403 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2370 1.31 - 1.44: 3734 1.44 - 1.57: 7991 1.57 - 1.69: 12 1.69 - 1.82: 174 Bond restraints: 14281 Sorted by residual: bond pdb=" C2' PCG B 904 " pdb=" C3' PCG B 904 " ideal model delta sigma weight residual 1.514 1.187 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C2' PCG A 901 " pdb=" C3' PCG A 901 " ideal model delta sigma weight residual 1.514 1.191 0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C2' PCG B 901 " pdb=" C3' PCG B 901 " ideal model delta sigma weight residual 1.514 1.192 0.322 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C2' PCG A 904 " pdb=" C3' PCG A 904 " ideal model delta sigma weight residual 1.514 1.192 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C3' PCG A 904 " pdb=" C4' PCG A 904 " ideal model delta sigma weight residual 1.519 1.812 -0.293 2.00e-02 2.50e+03 2.15e+02 ... (remaining 14276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 19087 2.53 - 5.06: 162 5.06 - 7.59: 40 7.59 - 10.12: 29 10.12 - 12.65: 2 Bond angle restraints: 19320 Sorted by residual: angle pdb=" C ARG A 40 " pdb=" CA ARG A 40 " pdb=" CB ARG A 40 " ideal model delta sigma weight residual 115.79 109.81 5.98 1.19e+00 7.06e-01 2.53e+01 angle pdb=" CB MET B 155 " pdb=" CG MET B 155 " pdb=" SD MET B 155 " ideal model delta sigma weight residual 112.70 125.35 -12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CA GLN A 285 " pdb=" CB GLN A 285 " pdb=" CG GLN A 285 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" C5' PCG A 904 " pdb=" O5' PCG A 904 " pdb=" PA PCG A 904 " ideal model delta sigma weight residual 121.82 111.33 10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C5' PCG A 901 " pdb=" O5' PCG A 901 " pdb=" PA PCG A 901 " ideal model delta sigma weight residual 121.82 111.78 10.04 3.00e+00 1.11e-01 1.12e+01 ... (remaining 19315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.23: 7542 20.23 - 40.45: 921 40.45 - 60.68: 197 60.68 - 80.90: 35 80.90 - 101.13: 11 Dihedral angle restraints: 8706 sinusoidal: 3702 harmonic: 5004 Sorted by residual: dihedral pdb=" CA TYR B 402 " pdb=" C TYR B 402 " pdb=" N ASN B 403 " pdb=" CA ASN B 403 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA PRO B 41 " pdb=" C PRO B 41 " pdb=" N GLU B 42 " pdb=" CA GLU B 42 " ideal model delta harmonic sigma weight residual 180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" C4' PCG B 904 " pdb=" C5' PCG B 904 " pdb=" O5' PCG B 904 " pdb=" PA PCG B 904 " ideal model delta sinusoidal sigma weight residual 53.73 -47.40 101.13 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 8703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2064 0.107 - 0.214: 28 0.214 - 0.321: 1 0.321 - 0.428: 7 0.428 - 0.535: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" PA PCG B 904 " pdb=" O2A PCG B 904 " pdb=" O3' PCG B 904 " pdb=" O5' PCG B 904 " both_signs ideal model delta sigma weight residual True 2.70 3.23 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" PA PCG A 904 " pdb=" O2A PCG A 904 " pdb=" O3' PCG A 904 " pdb=" O5' PCG A 904 " both_signs ideal model delta sigma weight residual True 2.70 3.22 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" PA PCG A 901 " pdb=" O2A PCG A 901 " pdb=" O3' PCG A 901 " pdb=" O5' PCG A 901 " both_signs ideal model delta sigma weight residual True 2.70 3.20 -0.51 2.00e-01 2.50e+01 6.38e+00 ... (remaining 2101 not shown) Planarity restraints: 2482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 132 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B 133 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 597 " 0.017 2.00e-02 2.50e+03 1.66e-02 4.13e+00 pdb=" CG HIS B 597 " -0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS B 597 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 597 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 597 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 597 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 19 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO D 20 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 20 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 20 " 0.024 5.00e-02 4.00e+02 ... (remaining 2479 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 131 2.60 - 3.18: 12054 3.18 - 3.75: 22446 3.75 - 4.33: 30129 4.33 - 4.90: 50991 Nonbonded interactions: 115751 Sorted by model distance: nonbonded pdb="MG MG B 903 " pdb=" O1A PCG B 904 " model vdw 2.028 2.170 nonbonded pdb=" OD2 ASP A 600 " pdb="ZN ZN A 902 " model vdw 2.075 2.230 nonbonded pdb="MG MG A 903 " pdb=" O1A PCG A 904 " model vdw 2.088 2.170 nonbonded pdb=" CG HIS B 597 " pdb="ZN ZN B 902 " model vdw 2.198 1.960 nonbonded pdb=" OD1 ASN A 607 " pdb=" NE2 GLN A 745 " model vdw 2.257 3.120 ... (remaining 115746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 12 through 86) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 36.680 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.896 14285 Z= 0.624 Angle : 0.698 12.652 19320 Z= 0.319 Chirality : 0.049 0.535 2104 Planarity : 0.003 0.051 2482 Dihedral : 17.944 101.128 5460 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 0.20 % Allowed : 18.69 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.21), residues: 1689 helix: 1.72 (0.17), residues: 954 sheet: 0.68 (0.44), residues: 139 loop : -0.16 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 697 HIS 0.017 0.001 HIS B 597 PHE 0.018 0.001 PHE B 163 TYR 0.011 0.001 TYR B 273 ARG 0.002 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.19835 ( 780) hydrogen bonds : angle 6.21806 ( 2259) metal coordination : bond 0.44828 ( 4) covalent geometry : bond 0.01148 (14281) covalent geometry : angle 0.69763 (19320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8012 (pttp) cc_final: 0.7803 (mtmm) REVERT: A 193 MET cc_start: 0.8306 (ptm) cc_final: 0.7805 (ppp) REVERT: A 222 MET cc_start: 0.8470 (mmm) cc_final: 0.7910 (mmt) REVERT: A 286 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8514 (mtpp) REVERT: A 296 MET cc_start: 0.7913 (mmm) cc_final: 0.7473 (mmm) REVERT: A 652 ARG cc_start: 0.7144 (tmm160) cc_final: 0.6936 (tmm160) REVERT: A 756 ASN cc_start: 0.8657 (t0) cc_final: 0.8412 (t0) REVERT: A 761 MET cc_start: 0.8545 (mtt) cc_final: 0.8309 (mtm) REVERT: B 96 MET cc_start: 0.8842 (mmm) cc_final: 0.8611 (mmm) REVERT: B 141 HIS cc_start: 0.8119 (t-170) cc_final: 0.7862 (t-170) REVERT: B 190 ILE cc_start: 0.8738 (mt) cc_final: 0.8530 (mp) REVERT: B 209 PHE cc_start: 0.8474 (t80) cc_final: 0.8273 (t80) REVERT: B 681 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8563 (mtpt) REVERT: B 808 LYS cc_start: 0.9008 (tptm) cc_final: 0.8233 (tptm) outliers start: 3 outliers final: 0 residues processed: 191 average time/residue: 0.3053 time to fit residues: 82.7669 Evaluate side-chains 141 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 131 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 202 HIS A 611 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS C 83 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.097299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076546 restraints weight = 35193.531| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.77 r_work: 0.3208 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14285 Z= 0.134 Angle : 0.530 6.016 19320 Z= 0.281 Chirality : 0.039 0.146 2104 Planarity : 0.004 0.054 2482 Dihedral : 4.830 40.492 1966 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 1.97 % Allowed : 17.44 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.21), residues: 1689 helix: 1.94 (0.17), residues: 963 sheet: 0.35 (0.42), residues: 140 loop : -0.04 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.006 0.001 HIS B 597 PHE 0.020 0.001 PHE B 209 TYR 0.026 0.001 TYR A 49 ARG 0.003 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 780) hydrogen bonds : angle 4.63939 ( 2259) metal coordination : bond 0.00993 ( 4) covalent geometry : bond 0.00290 (14281) covalent geometry : angle 0.52952 (19320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8220 (ptm) cc_final: 0.6815 (ppp) REVERT: A 286 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8511 (mtpp) REVERT: A 296 MET cc_start: 0.7654 (mmm) cc_final: 0.7379 (mmm) REVERT: A 700 TYR cc_start: 0.7059 (t80) cc_final: 0.6676 (t80) REVERT: A 756 ASN cc_start: 0.8763 (t0) cc_final: 0.8479 (t0) REVERT: B 681 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8498 (mtpp) REVERT: B 714 MET cc_start: 0.9077 (mmm) cc_final: 0.8828 (mmm) REVERT: B 759 MET cc_start: 0.8683 (mtt) cc_final: 0.8471 (mtm) REVERT: B 766 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7389 (mp0) REVERT: D 17 MET cc_start: 0.6618 (mmm) cc_final: 0.6402 (mmm) outliers start: 30 outliers final: 11 residues processed: 162 average time/residue: 0.2877 time to fit residues: 67.6749 Evaluate side-chains 135 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 4 optimal weight: 10.0000 chunk 32 optimal weight: 0.0170 chunk 131 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 144 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.098037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.077279 restraints weight = 35731.807| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.84 r_work: 0.3229 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14285 Z= 0.108 Angle : 0.493 8.164 19320 Z= 0.258 Chirality : 0.038 0.136 2104 Planarity : 0.004 0.053 2482 Dihedral : 4.760 39.578 1966 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 2.16 % Allowed : 16.79 % Favored : 81.05 % 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: 1.61 (0.21), residues: 1689 helix: 1.92 (0.17), residues: 962 sheet: 0.24 (0.41), residues: 140 loop : -0.07 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 559 HIS 0.008 0.001 HIS B 141 PHE 0.017 0.001 PHE B 209 TYR 0.015 0.001 TYR B 273 ARG 0.005 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 780) hydrogen bonds : angle 4.33773 ( 2259) metal coordination : bond 0.00284 ( 4) covalent geometry : bond 0.00236 (14281) covalent geometry : angle 0.49301 (19320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8115 (ptm) cc_final: 0.6929 (ppp) REVERT: A 286 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8598 (mtpp) REVERT: A 571 MET cc_start: 0.8766 (tpp) cc_final: 0.8527 (tpp) REVERT: A 638 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8884 (mt) REVERT: A 756 ASN cc_start: 0.8763 (t0) cc_final: 0.8483 (t0) REVERT: B 174 ASN cc_start: 0.6715 (OUTLIER) cc_final: 0.5831 (p0) REVERT: B 280 MET cc_start: 0.8322 (mmt) cc_final: 0.7963 (mmt) REVERT: B 671 LEU cc_start: 0.8270 (tt) cc_final: 0.8057 (mp) REVERT: B 681 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8378 (mtpp) REVERT: B 712 MET cc_start: 0.8261 (mpp) cc_final: 0.7816 (mpp) outliers start: 33 outliers final: 14 residues processed: 159 average time/residue: 0.2885 time to fit residues: 68.8057 Evaluate side-chains 141 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 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 69 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 729 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.097364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.076556 restraints weight = 35708.079| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.83 r_work: 0.3209 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14285 Z= 0.114 Angle : 0.490 6.604 19320 Z= 0.255 Chirality : 0.038 0.131 2104 Planarity : 0.004 0.053 2482 Dihedral : 4.676 39.671 1966 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.04 % Rotamer: Outliers : 2.10 % Allowed : 16.98 % Favored : 80.92 % 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: 1.67 (0.21), residues: 1689 helix: 1.99 (0.17), residues: 962 sheet: 0.19 (0.41), residues: 140 loop : -0.08 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 559 HIS 0.006 0.001 HIS B 141 PHE 0.015 0.001 PHE B 209 TYR 0.015 0.001 TYR B 273 ARG 0.005 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 780) hydrogen bonds : angle 4.20795 ( 2259) metal coordination : bond 0.00356 ( 4) covalent geometry : bond 0.00257 (14281) covalent geometry : angle 0.48987 (19320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.6670 (OUTLIER) cc_final: 0.6266 (m-40) REVERT: A 193 MET cc_start: 0.8145 (ptm) cc_final: 0.7089 (ppp) REVERT: A 638 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8916 (mt) REVERT: A 756 ASN cc_start: 0.8738 (t0) cc_final: 0.8469 (t0) REVERT: B 66 MET cc_start: 0.8049 (mtt) cc_final: 0.7820 (ttm) REVERT: B 681 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8367 (mtpp) REVERT: D 37 GLN cc_start: 0.6540 (pt0) cc_final: 0.6269 (pt0) outliers start: 32 outliers final: 16 residues processed: 154 average time/residue: 0.2852 time to fit residues: 65.9887 Evaluate side-chains 138 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 127 optimal weight: 0.0870 chunk 104 optimal weight: 4.9990 chunk 107 optimal weight: 0.0570 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 overall best weight: 1.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.096075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.075071 restraints weight = 36155.010| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.84 r_work: 0.3187 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14285 Z= 0.146 Angle : 0.509 8.854 19320 Z= 0.264 Chirality : 0.039 0.135 2104 Planarity : 0.004 0.057 2482 Dihedral : 4.753 40.410 1966 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 2.23 % Allowed : 17.25 % Favored : 80.52 % 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: 1.67 (0.21), residues: 1689 helix: 2.00 (0.17), residues: 962 sheet: 0.16 (0.41), residues: 140 loop : -0.09 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 559 HIS 0.005 0.001 HIS B 597 PHE 0.014 0.001 PHE B 209 TYR 0.015 0.001 TYR B 273 ARG 0.005 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 780) hydrogen bonds : angle 4.21350 ( 2259) metal coordination : bond 0.00439 ( 4) covalent geometry : bond 0.00339 (14281) covalent geometry : angle 0.50949 (19320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.6611 (OUTLIER) cc_final: 0.6240 (m-40) REVERT: A 638 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8893 (mt) REVERT: B 174 ASN cc_start: 0.6720 (OUTLIER) cc_final: 0.5984 (p0) REVERT: B 293 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7864 (tt) REVERT: B 681 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8360 (mtpp) REVERT: D 37 GLN cc_start: 0.6681 (pt0) cc_final: 0.6385 (pt0) outliers start: 34 outliers final: 18 residues processed: 154 average time/residue: 0.2714 time to fit residues: 62.0531 Evaluate side-chains 142 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 152 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.096696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.075924 restraints weight = 36503.880| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.86 r_work: 0.3197 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14285 Z= 0.117 Angle : 0.501 8.711 19320 Z= 0.258 Chirality : 0.038 0.141 2104 Planarity : 0.004 0.054 2482 Dihedral : 4.706 39.826 1966 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.16 % Allowed : 17.97 % 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: 1.72 (0.21), residues: 1689 helix: 2.06 (0.17), residues: 961 sheet: 0.14 (0.41), residues: 140 loop : -0.09 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 559 HIS 0.004 0.001 HIS B 658 PHE 0.014 0.001 PHE B 209 TYR 0.015 0.001 TYR B 273 ARG 0.007 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 780) hydrogen bonds : angle 4.15930 ( 2259) metal coordination : bond 0.00269 ( 4) covalent geometry : bond 0.00270 (14281) covalent geometry : angle 0.50060 (19320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7912 (mtp) cc_final: 0.7683 (mtp) REVERT: A 176 ASN cc_start: 0.6588 (OUTLIER) cc_final: 0.6227 (m-40) REVERT: A 193 MET cc_start: 0.8294 (ptm) cc_final: 0.7150 (ppp) REVERT: A 638 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8847 (mt) REVERT: A 793 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 174 ASN cc_start: 0.6727 (OUTLIER) cc_final: 0.5987 (p0) REVERT: B 293 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8032 (tt) REVERT: B 681 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8419 (mtpt) REVERT: D 37 GLN cc_start: 0.6679 (pt0) cc_final: 0.6359 (pt0) outliers start: 33 outliers final: 19 residues processed: 154 average time/residue: 0.3389 time to fit residues: 78.6590 Evaluate side-chains 145 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 133 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.097085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076214 restraints weight = 36092.981| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.86 r_work: 0.3204 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14285 Z= 0.109 Angle : 0.498 9.369 19320 Z= 0.256 Chirality : 0.038 0.167 2104 Planarity : 0.004 0.054 2482 Dihedral : 4.628 39.258 1966 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.03 % Allowed : 18.30 % Favored : 79.67 % 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: 1.76 (0.21), residues: 1689 helix: 2.10 (0.17), residues: 961 sheet: 0.16 (0.41), residues: 140 loop : -0.07 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 559 HIS 0.004 0.001 HIS B 658 PHE 0.016 0.001 PHE B 588 TYR 0.017 0.001 TYR B 783 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 780) hydrogen bonds : angle 4.11933 ( 2259) metal coordination : bond 0.00209 ( 4) covalent geometry : bond 0.00250 (14281) covalent geometry : angle 0.49785 (19320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7913 (mtp) cc_final: 0.7698 (mtp) REVERT: A 176 ASN cc_start: 0.6553 (OUTLIER) cc_final: 0.6223 (m-40) REVERT: A 193 MET cc_start: 0.8322 (ptm) cc_final: 0.7088 (ppp) REVERT: A 638 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8836 (mt) REVERT: A 793 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 26 LYS cc_start: 0.8053 (tmtt) cc_final: 0.7534 (tmtt) REVERT: B 174 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.5998 (p0) REVERT: B 209 PHE cc_start: 0.8374 (t80) cc_final: 0.7899 (t80) REVERT: B 293 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8013 (tt) REVERT: B 681 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8346 (mtpp) REVERT: D 37 GLN cc_start: 0.6686 (pt0) cc_final: 0.6483 (pt0) outliers start: 31 outliers final: 18 residues processed: 152 average time/residue: 0.2973 time to fit residues: 68.4131 Evaluate side-chains 142 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.094257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072973 restraints weight = 36100.233| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.84 r_work: 0.3151 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14285 Z= 0.206 Angle : 0.580 9.449 19320 Z= 0.298 Chirality : 0.041 0.185 2104 Planarity : 0.004 0.055 2482 Dihedral : 4.950 41.505 1966 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.64 % Allowed : 18.43 % Favored : 79.93 % 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: 1.52 (0.21), residues: 1689 helix: 1.89 (0.17), residues: 962 sheet: 0.14 (0.41), residues: 140 loop : -0.19 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 697 HIS 0.007 0.001 HIS A 660 PHE 0.024 0.002 PHE B 588 TYR 0.018 0.002 TYR B 97 ARG 0.009 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 780) hydrogen bonds : angle 4.31115 ( 2259) metal coordination : bond 0.00539 ( 4) covalent geometry : bond 0.00483 (14281) covalent geometry : angle 0.58013 (19320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 712 MET cc_start: 0.8615 (ttp) cc_final: 0.8310 (ttp) REVERT: B 26 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7875 (tmtt) REVERT: B 174 ASN cc_start: 0.6970 (OUTLIER) cc_final: 0.6296 (p0) REVERT: B 209 PHE cc_start: 0.8374 (t80) cc_final: 0.7917 (t80) REVERT: B 293 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7891 (tt) REVERT: B 681 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8379 (mtpp) REVERT: C 83 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6524 (tp-100) REVERT: D 37 GLN cc_start: 0.6856 (pt0) cc_final: 0.6637 (pt0) outliers start: 25 outliers final: 17 residues processed: 146 average time/residue: 0.2570 time to fit residues: 56.3190 Evaluate side-chains 138 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 6 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 127 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 164 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.095734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.074690 restraints weight = 36014.380| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.84 r_work: 0.3166 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14285 Z= 0.129 Angle : 0.533 10.228 19320 Z= 0.273 Chirality : 0.039 0.190 2104 Planarity : 0.004 0.053 2482 Dihedral : 4.780 39.845 1966 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.64 % Allowed : 18.75 % Favored : 79.61 % 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: 1.63 (0.21), residues: 1689 helix: 1.99 (0.17), residues: 962 sheet: 0.06 (0.40), residues: 140 loop : -0.12 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 559 HIS 0.003 0.001 HIS B 597 PHE 0.022 0.001 PHE B 588 TYR 0.016 0.001 TYR B 783 ARG 0.011 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 780) hydrogen bonds : angle 4.20830 ( 2259) metal coordination : bond 0.00296 ( 4) covalent geometry : bond 0.00301 (14281) covalent geometry : angle 0.53324 (19320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.6545 (OUTLIER) cc_final: 0.6227 (m-40) REVERT: A 193 MET cc_start: 0.8325 (ptm) cc_final: 0.7189 (ppp) REVERT: A 712 MET cc_start: 0.8746 (ttp) cc_final: 0.8401 (ttp) REVERT: B 72 MET cc_start: 0.8496 (tmm) cc_final: 0.8181 (tmm) REVERT: B 174 ASN cc_start: 0.6923 (OUTLIER) cc_final: 0.6261 (p0) REVERT: B 209 PHE cc_start: 0.8262 (t80) cc_final: 0.7932 (t80) REVERT: B 293 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7913 (tt) REVERT: B 681 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8382 (mtpp) REVERT: B 697 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: D 37 GLN cc_start: 0.6878 (pt0) cc_final: 0.6673 (pt0) outliers start: 25 outliers final: 18 residues processed: 145 average time/residue: 0.2698 time to fit residues: 60.7383 Evaluate side-chains 140 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 113 optimal weight: 0.0670 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.095235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074120 restraints weight = 36288.608| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.86 r_work: 0.3162 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14285 Z= 0.144 Angle : 0.549 10.488 19320 Z= 0.281 Chirality : 0.039 0.216 2104 Planarity : 0.004 0.053 2482 Dihedral : 4.759 39.875 1966 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.44 % Allowed : 19.02 % Favored : 79.54 % 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: 1.61 (0.21), residues: 1689 helix: 1.98 (0.17), residues: 962 sheet: 0.06 (0.40), residues: 140 loop : -0.14 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 697 HIS 0.005 0.001 HIS B 561 PHE 0.022 0.001 PHE B 588 TYR 0.015 0.001 TYR B 273 ARG 0.010 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 780) hydrogen bonds : angle 4.21737 ( 2259) metal coordination : bond 0.00349 ( 4) covalent geometry : bond 0.00338 (14281) covalent geometry : angle 0.54879 (19320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8355 (mtm110) cc_final: 0.7918 (ptm-80) REVERT: A 193 MET cc_start: 0.8257 (ptm) cc_final: 0.7088 (ppp) REVERT: A 712 MET cc_start: 0.8592 (ttp) cc_final: 0.8357 (ttp) REVERT: B 72 MET cc_start: 0.8505 (tmm) cc_final: 0.8198 (tmm) REVERT: B 174 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6338 (p0) REVERT: B 209 PHE cc_start: 0.8260 (t80) cc_final: 0.8034 (t80) REVERT: B 293 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7913 (tt) REVERT: B 681 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8382 (mtpp) REVERT: B 697 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: D 37 GLN cc_start: 0.6875 (pt0) cc_final: 0.6664 (pt0) outliers start: 22 outliers final: 18 residues processed: 142 average time/residue: 0.2827 time to fit residues: 60.5390 Evaluate side-chains 143 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 129 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.096390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075445 restraints weight = 36206.904| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.86 r_work: 0.3186 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14285 Z= 0.114 Angle : 0.535 10.224 19320 Z= 0.272 Chirality : 0.038 0.217 2104 Planarity : 0.004 0.052 2482 Dihedral : 4.632 38.814 1966 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.57 % Allowed : 19.08 % Favored : 79.34 % 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: 1689 helix: 2.06 (0.17), residues: 961 sheet: 0.02 (0.40), residues: 140 loop : -0.07 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.003 0.001 HIS B 658 PHE 0.018 0.001 PHE B 588 TYR 0.017 0.001 TYR B 783 ARG 0.008 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 780) hydrogen bonds : angle 4.13985 ( 2259) metal coordination : bond 0.00199 ( 4) covalent geometry : bond 0.00266 (14281) covalent geometry : angle 0.53514 (19320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6688.55 seconds wall clock time: 117 minutes 43.53 seconds (7063.53 seconds total)