Starting phenix.real_space_refine on Wed Mar 12 01:40:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3h_29699/03_2025/8g3h_29699_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3h_29699/03_2025/8g3h_29699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3h_29699/03_2025/8g3h_29699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3h_29699/03_2025/8g3h_29699.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3h_29699/03_2025/8g3h_29699_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3h_29699/03_2025/8g3h_29699_neut.cif" } resolution = 3.6 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= 0.019 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 Co 1 6.85 5 Zn 1 6.06 5 P 1 5.49 5 S 26 5.16 5 C 4159 2.51 5 N 1125 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6541 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6449 Classifications: {'peptide': 841} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 39, 'TRANS': 801} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {' ZN': 1, 'B12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unsupported chir.volume_sign: {'cros': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1673 SG CYS A 256 34.318 42.889 80.873 1.00 12.37 S ATOM 2190 SG CYS A 323 34.049 43.743 84.392 1.00 19.07 S Time building chain proxies: 5.50, per 1000 atoms: 0.84 Number of scatterers: 6541 At special positions: 0 Unit cell: (64.146, 90.8735, 112.256, 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 1 29.99 Co 1 26.99 S 26 16.00 P 1 15.00 O 1228 8.00 N 1125 7.00 C 4159 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 922.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 256 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 323 " 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 54.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.839A pdb=" N THR A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 100 removed outlier: 3.656A pdb=" N VAL A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 125 through 142 Processing helix chain 'A' and resid 165 through 183 removed outlier: 3.705A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.682A pdb=" N LEU A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 6.119A pdb=" N ALA A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 4.352A pdb=" N THR A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.937A pdb=" N ILE A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.827A pdb=" N GLU A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 removed outlier: 3.551A pdb=" N ILE A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 436 removed outlier: 3.711A pdb=" N LYS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N THR A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.915A pdb=" N MET A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 485 removed outlier: 4.405A pdb=" N LYS A 474 " --> pdb=" O ASP A 470 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 522 removed outlier: 3.870A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 546 through 560 removed outlier: 3.903A pdb=" N GLU A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 580 through 595 Processing helix chain 'A' and resid 605 through 609 removed outlier: 3.866A pdb=" N ILE A 609 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 629 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 662 through 674 Processing helix chain 'A' and resid 678 through 690 Processing helix chain 'A' and resid 691 through 698 Processing helix chain 'A' and resid 698 through 713 removed outlier: 6.001A pdb=" N MET A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 736 removed outlier: 3.600A pdb=" N ALA A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 772 removed outlier: 3.786A pdb=" N ILE A 769 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU A 770 " --> pdb=" O VAL A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 797 removed outlier: 3.871A pdb=" N MET A 789 " --> pdb=" O PRO A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 824 removed outlier: 4.243A pdb=" N THR A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN A 812 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 848 removed outlier: 5.300A pdb=" N GLU A 843 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU A 844 " --> pdb=" O TYR A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.138A pdb=" N LEU A 50 " --> pdb=" O VAL A 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.459A pdb=" N VAL A 148 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A 189 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY A 150 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A 191 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 188 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN A 222 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 190 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 253 Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 290 Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA6, first strand: chain 'A' and resid 440 through 442 removed outlier: 5.990A pdb=" N LEU A 410 " --> pdb=" O MET A 441 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 370 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP A 411 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 372 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER A 413 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ARG A 374 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 373 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 567 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 603 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU A 569 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N PHE A 530 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY A 570 " --> pdb=" O PHE A 530 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 491 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.701A pdb=" N LYS A 748 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY A 802 " --> pdb=" O LYS A 748 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 750 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A 801 " --> pdb=" O ILE A 831 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 807 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: 2.02 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.33: 1750 1.33 - 1.50: 2012 1.50 - 1.67: 2846 1.67 - 1.84: 47 1.84 - 2.01: 4 Bond restraints: 6659 Sorted by residual: bond pdb=" C3R B12 A1202 " pdb=" O2 B12 A1202 " ideal model delta sigma weight residual 1.426 1.651 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C15 B12 A1202 " pdb=" C53 B12 A1202 " ideal model delta sigma weight residual 1.500 1.685 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" C4 B12 A1202 " pdb=" N21 B12 A1202 " ideal model delta sigma weight residual 1.416 1.235 0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C49 B12 A1202 " pdb=" C50 B12 A1202 " ideal model delta sigma weight residual 1.510 1.337 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C5R B12 A1202 " pdb=" O8R B12 A1202 " ideal model delta sigma weight residual 1.432 1.267 0.165 2.00e-02 2.50e+03 6.84e+01 ... (remaining 6654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 8852 5.65 - 11.29: 161 11.29 - 16.94: 28 16.94 - 22.59: 5 22.59 - 28.23: 3 Bond angle restraints: 9049 Sorted by residual: angle pdb=" N ALA A 855 " pdb=" CA ALA A 855 " pdb=" C ALA A 855 " ideal model delta sigma weight residual 110.24 83.37 26.87 1.30e+00 5.92e-01 4.27e+02 angle pdb=" C ALA A 855 " pdb=" CA ALA A 855 " pdb=" CB ALA A 855 " ideal model delta sigma weight residual 109.64 137.87 -28.23 1.77e+00 3.19e-01 2.54e+02 angle pdb=" N VAL A 51 " pdb=" CA VAL A 51 " pdb=" C VAL A 51 " ideal model delta sigma weight residual 108.17 123.43 -15.26 1.40e+00 5.10e-01 1.19e+02 angle pdb=" C LEU A 562 " pdb=" N PRO A 563 " pdb=" CA PRO A 563 " ideal model delta sigma weight residual 120.03 111.29 8.74 9.90e-01 1.02e+00 7.79e+01 angle pdb=" C18 B12 A1202 " pdb=" C19 B12 A1202 " pdb=" N24 B12 A1202 " ideal model delta sigma weight residual 120.00 94.26 25.74 3.00e+00 1.11e-01 7.36e+01 ... (remaining 9044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 3828 29.20 - 58.41: 191 58.41 - 87.61: 22 87.61 - 116.81: 1 116.81 - 146.02: 2 Dihedral angle restraints: 4044 sinusoidal: 1642 harmonic: 2402 Sorted by residual: dihedral pdb=" C ARG A 839 " pdb=" N ARG A 839 " pdb=" CA ARG A 839 " pdb=" CB ARG A 839 " ideal model delta harmonic sigma weight residual -122.60 -142.45 19.85 0 2.50e+00 1.60e-01 6.30e+01 dihedral pdb=" C ALA A 855 " pdb=" N ALA A 855 " pdb=" CA ALA A 855 " pdb=" CB ALA A 855 " ideal model delta harmonic sigma weight residual -122.60 -139.40 16.80 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" C3R B12 A1202 " pdb=" O2 B12 A1202 " pdb=" P B12 A1202 " pdb=" O4 B12 A1202 " ideal model delta sinusoidal sigma weight residual 60.00 -153.98 -146.02 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 4041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.110: 1034 1.110 - 2.220: 2 2.220 - 3.330: 2 3.330 - 4.441: 0 4.441 - 5.551: 1 Chirality restraints: 1039 Sorted by residual: chirality pdb=" C12 B12 A1202 " pdb=" C11 B12 A1202 " pdb=" C46 B12 A1202 " pdb=" C47 B12 A1202 " both_signs ideal model delta sigma weight residual False -2.64 2.91 -5.55 2.00e-01 2.50e+01 7.70e+02 chirality pdb=" N21 B12 A1202 " pdb=" C1 B12 A1202 " pdb=" C4 B12 A1202 " pdb="CO B12 A1202 " both_signs ideal model delta sigma weight residual False -3.05 0.08 -3.13 2.00e-01 2.50e+01 2.44e+02 chirality pdb=" N22 B12 A1202 " pdb=" C6 B12 A1202 " pdb=" C9 B12 A1202 " pdb="CO B12 A1202 " both_signs ideal model delta sigma weight residual False -2.93 -0.18 -2.75 2.00e-01 2.50e+01 1.89e+02 ... (remaining 1036 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C35 B12 A1202 " -0.186 2.00e-02 2.50e+03 1.40e-01 2.94e+02 pdb=" C4 B12 A1202 " 0.093 2.00e-02 2.50e+03 pdb=" C5 B12 A1202 " 0.145 2.00e-02 2.50e+03 pdb=" C6 B12 A1202 " 0.038 2.00e-02 2.50e+03 pdb=" C7 B12 A1202 " 0.110 2.00e-02 2.50e+03 pdb=" N22 B12 A1202 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1R B12 A1202 " 0.040 2.00e-02 2.50e+03 9.59e-02 2.76e+02 pdb=" C2B B12 A1202 " -0.137 2.00e-02 2.50e+03 pdb=" C4B B12 A1202 " -0.016 2.00e-02 2.50e+03 pdb=" C5B B12 A1202 " 0.036 2.00e-02 2.50e+03 pdb=" C5M B12 A1202 " 0.094 2.00e-02 2.50e+03 pdb=" C6B B12 A1202 " 0.060 2.00e-02 2.50e+03 pdb=" C6M B12 A1202 " -0.230 2.00e-02 2.50e+03 pdb=" C7B B12 A1202 " 0.088 2.00e-02 2.50e+03 pdb=" C8B B12 A1202 " 0.072 2.00e-02 2.50e+03 pdb=" C9B B12 A1202 " -0.006 2.00e-02 2.50e+03 pdb=" N1B B12 A1202 " 0.070 2.00e-02 2.50e+03 pdb=" N3B B12 A1202 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 B12 A1202 " 0.110 2.00e-02 2.50e+03 1.60e-01 2.55e+02 pdb=" C18 B12 A1202 " 0.094 2.00e-02 2.50e+03 pdb=" C19 B12 A1202 " -0.275 2.00e-02 2.50e+03 pdb=" N24 B12 A1202 " 0.071 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 684 2.76 - 3.30: 7130 3.30 - 3.83: 10904 3.83 - 4.37: 14047 4.37 - 4.90: 22381 Nonbonded interactions: 55146 Sorted by model distance: nonbonded pdb=" N ALA A 855 " pdb=" O ALA A 855 " model vdw 2.228 2.496 nonbonded pdb=" N GLY A 321 " pdb=" O GLY A 321 " model vdw 2.275 2.496 nonbonded pdb=" N MET A 803 " pdb=" O MET A 803 " model vdw 2.375 2.496 nonbonded pdb=" N ARG A 559 " pdb=" N GLU A 560 " model vdw 2.393 2.560 nonbonded pdb=" C TYR A 854 " pdb=" C ALA A 855 " model vdw 2.394 2.800 ... (remaining 55141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 4.600 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: 0.040 Set scattering table: 0.060 Process input model: 22.400 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5129 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 : 0.016 0.225 6659 Z= 1.047 Angle : 2.317 28.234 9049 Z= 1.409 Chirality : 0.258 5.551 1039 Planarity : 0.017 0.160 1180 Dihedral : 17.251 146.016 2506 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.37 % Allowed : 14.61 % Favored : 81.02 % Cbeta Deviations : 1.17 % 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: -4.03 (0.24), residues: 839 helix: -2.85 (0.19), residues: 387 sheet: -1.65 (0.76), residues: 47 loop : -2.56 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.013 TRP A 166 HIS 0.013 0.004 HIS A 759 PHE 0.096 0.018 PHE A 52 TYR 0.091 0.013 TYR A 854 ARG 0.013 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.5203 (mt) cc_final: 0.5002 (mt) REVERT: A 276 ARG cc_start: 0.4509 (mtm110) cc_final: 0.4093 (mmm160) REVERT: A 367 SER cc_start: 0.6095 (OUTLIER) cc_final: 0.5842 (t) REVERT: A 405 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: A 464 ASN cc_start: 0.5844 (m-40) cc_final: 0.5216 (t0) REVERT: A 789 MET cc_start: 0.6153 (ttt) cc_final: 0.5770 (ttm) REVERT: A 820 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.3795 (p90) REVERT: A 865 MET cc_start: 0.3583 (mmm) cc_final: 0.3373 (mmt) outliers start: 29 outliers final: 6 residues processed: 168 average time/residue: 0.2469 time to fit residues: 51.4995 Evaluate side-chains 103 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 198 GLN A 772 ASN ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.229527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.208796 restraints weight = 8491.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.213001 restraints weight = 5357.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.216119 restraints weight = 3705.461| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6659 Z= 0.298 Angle : 1.160 30.677 9049 Z= 0.512 Chirality : 0.094 2.381 1039 Planarity : 0.006 0.062 1180 Dihedral : 11.827 135.664 982 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.82 % Allowed : 16.42 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.26), residues: 839 helix: -1.22 (0.23), residues: 386 sheet: -2.17 (0.57), residues: 76 loop : -1.73 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 166 HIS 0.010 0.002 HIS A 759 PHE 0.018 0.002 PHE A 475 TYR 0.026 0.002 TYR A 820 ARG 0.007 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6910 (mmt) cc_final: 0.6382 (mmt) REVERT: A 80 GLU cc_start: 0.3299 (OUTLIER) cc_final: 0.2177 (tt0) REVERT: A 276 ARG cc_start: 0.5001 (mtm110) cc_final: 0.4147 (mmt180) REVERT: A 367 SER cc_start: 0.5227 (OUTLIER) cc_final: 0.4830 (t) REVERT: A 464 ASN cc_start: 0.6303 (m-40) cc_final: 0.5443 (t0) REVERT: A 513 MET cc_start: 0.1858 (ptp) cc_final: 0.1627 (ptm) REVERT: A 765 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.5086 (mm) REVERT: A 789 MET cc_start: 0.6013 (ttt) cc_final: 0.5683 (ttm) outliers start: 32 outliers final: 17 residues processed: 130 average time/residue: 0.1933 time to fit residues: 33.6640 Evaluate side-chains 109 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.228452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.206476 restraints weight = 8649.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.210597 restraints weight = 5541.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.213657 restraints weight = 3881.421| |-----------------------------------------------------------------------------| r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6659 Z= 0.270 Angle : 1.084 30.652 9049 Z= 0.468 Chirality : 0.093 2.428 1039 Planarity : 0.006 0.057 1180 Dihedral : 10.796 131.196 977 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.07 % Allowed : 17.77 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.27), residues: 839 helix: -0.72 (0.24), residues: 389 sheet: -2.19 (0.58), residues: 76 loop : -1.61 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 166 HIS 0.008 0.001 HIS A 759 PHE 0.019 0.002 PHE A 643 TYR 0.018 0.002 TYR A 820 ARG 0.004 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.5238 (mtm110) cc_final: 0.4152 (mmt180) REVERT: A 412 LEU cc_start: 0.7531 (tp) cc_final: 0.7085 (pt) REVERT: A 464 ASN cc_start: 0.6078 (m-40) cc_final: 0.5536 (t0) REVERT: A 610 LEU cc_start: 0.6205 (pt) cc_final: 0.5682 (mt) REVERT: A 765 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.5000 (mm) REVERT: A 786 ILE cc_start: 0.6731 (pt) cc_final: 0.6096 (mp) REVERT: A 789 MET cc_start: 0.5755 (ttt) cc_final: 0.5493 (mtp) REVERT: A 820 TYR cc_start: 0.6324 (OUTLIER) cc_final: 0.4128 (p90) outliers start: 27 outliers final: 14 residues processed: 118 average time/residue: 0.1626 time to fit residues: 26.7597 Evaluate side-chains 109 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PRO Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.0770 chunk 79 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.0980 overall best weight: 0.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.233514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.211262 restraints weight = 8682.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.215536 restraints weight = 5573.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.218673 restraints weight = 3887.033| |-----------------------------------------------------------------------------| r_work (final): 0.4704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5296 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6659 Z= 0.199 Angle : 1.023 30.981 9049 Z= 0.429 Chirality : 0.091 2.407 1039 Planarity : 0.005 0.060 1180 Dihedral : 10.161 126.511 976 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.46 % Allowed : 19.88 % Favored : 76.66 % 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 (0.28), residues: 839 helix: -0.39 (0.25), residues: 398 sheet: -2.08 (0.58), residues: 78 loop : -1.50 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 166 HIS 0.013 0.002 HIS A 799 PHE 0.013 0.001 PHE A 643 TYR 0.024 0.002 TYR A 269 ARG 0.003 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 LEU cc_start: 0.7741 (tp) cc_final: 0.7103 (pt) REVERT: A 675 LYS cc_start: 0.6964 (mmtt) cc_final: 0.5943 (mmtt) REVERT: A 820 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.3972 (p90) outliers start: 23 outliers final: 15 residues processed: 116 average time/residue: 0.1508 time to fit residues: 24.7100 Evaluate side-chains 101 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 820 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 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 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.225346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.203225 restraints weight = 8601.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.207271 restraints weight = 5570.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.210274 restraints weight = 3952.372| |-----------------------------------------------------------------------------| r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6659 Z= 0.291 Angle : 1.064 31.131 9049 Z= 0.451 Chirality : 0.091 2.389 1039 Planarity : 0.006 0.068 1180 Dihedral : 10.270 122.695 976 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.77 % Allowed : 21.08 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.27), residues: 839 helix: -0.51 (0.24), residues: 396 sheet: -2.63 (0.57), residues: 79 loop : -1.55 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 166 HIS 0.005 0.002 HIS A 759 PHE 0.017 0.002 PHE A 711 TYR 0.017 0.002 TYR A 820 ARG 0.005 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 669 ARG cc_start: 0.4482 (mtt90) cc_final: 0.4196 (mtt90) outliers start: 25 outliers final: 18 residues processed: 108 average time/residue: 0.1516 time to fit residues: 23.4421 Evaluate side-chains 101 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** 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 = 0.4764 r_free = 0.4764 target = 0.225188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.202646 restraints weight = 8672.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.206944 restraints weight = 5581.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.210054 restraints weight = 3922.568| |-----------------------------------------------------------------------------| r_work (final): 0.4633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6659 Z= 0.259 Angle : 1.047 31.478 9049 Z= 0.441 Chirality : 0.090 2.375 1039 Planarity : 0.005 0.066 1180 Dihedral : 10.065 121.802 976 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.37 % Allowed : 21.69 % Favored : 73.95 % 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: -1.88 (0.27), residues: 839 helix: -0.48 (0.24), residues: 398 sheet: -2.68 (0.57), residues: 79 loop : -1.69 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 166 HIS 0.006 0.002 HIS A 759 PHE 0.012 0.002 PHE A 643 TYR 0.017 0.001 TYR A 820 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6413 (mp0) cc_final: 0.6079 (tp30) REVERT: A 210 MET cc_start: 0.3511 (mtt) cc_final: 0.3023 (mtp) REVERT: A 412 LEU cc_start: 0.7636 (tp) cc_final: 0.6866 (pt) REVERT: A 610 LEU cc_start: 0.6013 (pt) cc_final: 0.5536 (mt) REVERT: A 669 ARG cc_start: 0.4609 (mtt90) cc_final: 0.4406 (mtt90) REVERT: A 820 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.4738 (p90) outliers start: 29 outliers final: 19 residues processed: 113 average time/residue: 0.1644 time to fit residues: 26.3755 Evaluate side-chains 105 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 57 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** 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 = 0.4839 r_free = 0.4839 target = 0.232265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.213928 restraints weight = 8446.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.216816 restraints weight = 5927.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.219063 restraints weight = 4431.632| |-----------------------------------------------------------------------------| r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5524 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6659 Z= 0.282 Angle : 1.057 31.356 9049 Z= 0.448 Chirality : 0.090 2.377 1039 Planarity : 0.005 0.067 1180 Dihedral : 10.051 121.331 976 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.07 % Allowed : 23.34 % Favored : 72.59 % 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: -1.98 (0.27), residues: 839 helix: -0.60 (0.24), residues: 398 sheet: -2.72 (0.59), residues: 71 loop : -1.73 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 166 HIS 0.006 0.002 HIS A 521 PHE 0.023 0.002 PHE A 643 TYR 0.018 0.002 TYR A 820 ARG 0.004 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.3356 (mtt) cc_final: 0.2882 (mtp) REVERT: A 231 MET cc_start: 0.7014 (mtt) cc_final: 0.6613 (mtt) REVERT: A 610 LEU cc_start: 0.6000 (pt) cc_final: 0.5697 (mt) REVERT: A 726 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7133 (mp0) REVERT: A 768 ILE cc_start: 0.7307 (tp) cc_final: 0.7022 (pt) REVERT: A 820 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.5165 (p90) outliers start: 27 outliers final: 21 residues processed: 106 average time/residue: 0.1588 time to fit residues: 24.3711 Evaluate side-chains 106 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** 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 = 0.4735 r_free = 0.4735 target = 0.222157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.199856 restraints weight = 8692.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.204056 restraints weight = 5539.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.207131 restraints weight = 3869.450| |-----------------------------------------------------------------------------| r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6659 Z= 0.283 Angle : 1.056 31.303 9049 Z= 0.446 Chirality : 0.090 2.380 1039 Planarity : 0.005 0.068 1180 Dihedral : 10.012 120.943 976 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.22 % Allowed : 23.95 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.27), residues: 839 helix: -0.56 (0.24), residues: 392 sheet: -2.75 (0.58), residues: 71 loop : -1.58 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.007 0.002 HIS A 521 PHE 0.022 0.002 PHE A 643 TYR 0.018 0.002 TYR A 820 ARG 0.005 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.3651 (mtt) cc_final: 0.3175 (mtp) REVERT: A 726 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7242 (mp0) REVERT: A 820 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.4870 (p90) outliers start: 28 outliers final: 21 residues processed: 108 average time/residue: 0.1491 time to fit residues: 23.1254 Evaluate side-chains 108 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 0.0270 chunk 73 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** 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 = 0.4731 r_free = 0.4731 target = 0.222393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.200021 restraints weight = 8868.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.204150 restraints weight = 5695.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.207179 restraints weight = 3994.450| |-----------------------------------------------------------------------------| r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6659 Z= 0.267 Angle : 1.047 31.249 9049 Z= 0.443 Chirality : 0.089 2.383 1039 Planarity : 0.005 0.058 1180 Dihedral : 9.927 120.010 976 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.22 % Allowed : 23.95 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.27), residues: 839 helix: -0.54 (0.24), residues: 398 sheet: -2.36 (0.59), residues: 72 loop : -1.58 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 166 HIS 0.007 0.001 HIS A 521 PHE 0.023 0.002 PHE A 643 TYR 0.017 0.001 TYR A 820 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.3657 (mtt) cc_final: 0.3197 (mtp) REVERT: A 412 LEU cc_start: 0.7955 (tt) cc_final: 0.7624 (pt) REVERT: A 726 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7191 (mp0) REVERT: A 820 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.5128 (p90) outliers start: 28 outliers final: 22 residues processed: 106 average time/residue: 0.1626 time to fit residues: 24.7108 Evaluate side-chains 108 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 0.0370 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** 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 = 0.4753 r_free = 0.4753 target = 0.225197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.203887 restraints weight = 8778.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.207901 restraints weight = 5573.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.210776 restraints weight = 3888.246| |-----------------------------------------------------------------------------| r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6659 Z= 0.232 Angle : 1.034 31.027 9049 Z= 0.433 Chirality : 0.089 2.394 1039 Planarity : 0.005 0.060 1180 Dihedral : 9.762 118.569 976 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.61 % Allowed : 25.15 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.28), residues: 839 helix: -0.42 (0.24), residues: 399 sheet: -2.39 (0.58), residues: 72 loop : -1.56 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 166 HIS 0.008 0.001 HIS A 521 PHE 0.024 0.001 PHE A 643 TYR 0.029 0.002 TYR A 97 ARG 0.005 0.000 ARG A 670 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.3686 (mtt) cc_final: 0.3174 (mtp) REVERT: A 726 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7154 (mp0) REVERT: A 820 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.5283 (p90) outliers start: 24 outliers final: 20 residues processed: 99 average time/residue: 0.1591 time to fit residues: 22.3089 Evaluate side-chains 96 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** 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 = 0.4736 r_free = 0.4736 target = 0.222951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.201662 restraints weight = 8804.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.205586 restraints weight = 5626.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.208429 restraints weight = 3965.260| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6659 Z= 0.264 Angle : 1.053 31.315 9049 Z= 0.443 Chirality : 0.089 2.381 1039 Planarity : 0.005 0.061 1180 Dihedral : 9.825 118.077 976 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.46 % Allowed : 25.15 % Favored : 71.39 % 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 (0.28), residues: 839 helix: -0.48 (0.24), residues: 399 sheet: -2.30 (0.59), residues: 72 loop : -1.51 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.008 0.002 HIS A 521 PHE 0.023 0.002 PHE A 643 TYR 0.027 0.002 TYR A 97 ARG 0.007 0.000 ARG A 670 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.80 seconds wall clock time: 41 minutes 45.79 seconds (2505.79 seconds total)