Starting phenix.real_space_refine on Wed Feb 12 01:59:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3h_29699/02_2025/8g3h_29699_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3h_29699/02_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_29699/02_2025/8g3h_29699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3h_29699/02_2025/8g3h_29699.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3h_29699/02_2025/8g3h_29699_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3h_29699/02_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-5592/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: 5.01, per 1000 atoms: 0.77 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: 1.90 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.73 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: 1.81 Time building geometry restraints manager: 2.10 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: 3.480 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: 0.060 Set scattering table: 0.060 Process input model: 20.910 Find NCS groups from input model: 0.050 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- 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 : 0.676 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: 0.2686 time to fit residues: 56.3858 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 : 0.755 ------------------------------------------------------------------------------- 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 = 0.208795 restraints weight = 8491.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.213092 restraints weight = 5355.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.216196 restraints weight = 3683.842| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 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 : 11.827 135.663 982 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 : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6909 (mmt) cc_final: 0.6381 (mmt) REVERT: A 80 GLU cc_start: 0.3299 (OUTLIER) cc_final: 0.2177 (tt0) REVERT: A 276 ARG cc_start: 0.5003 (mtm110) cc_final: 0.4147 (mmt180) REVERT: A 367 SER cc_start: 0.5225 (OUTLIER) cc_final: 0.4829 (t) REVERT: A 464 ASN cc_start: 0.6305 (m-40) cc_final: 0.5442 (t0) REVERT: A 513 MET cc_start: 0.1860 (ptp) cc_final: 0.1629 (ptm) REVERT: A 765 LEU cc_start: 0.5318 (OUTLIER) cc_final: 0.5085 (mm) REVERT: A 789 MET cc_start: 0.6012 (ttt) cc_final: 0.5682 (ttm) outliers start: 32 outliers final: 17 residues processed: 130 average time/residue: 0.1951 time to fit residues: 33.6697 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 : 0.709 ------------------------------------------------------------------------------- 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: 0.0970 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.228518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.206904 restraints weight = 8546.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.211069 restraints weight = 5425.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.214076 restraints weight = 3777.950| |-----------------------------------------------------------------------------| r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5413 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6659 Z= 0.275 Angle : 1.084 31.102 9049 Z= 0.467 Chirality : 0.092 2.406 1039 Planarity : 0.006 0.055 1180 Dihedral : 10.868 131.725 977 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.07 % Allowed : 18.22 % Favored : 77.71 % 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: -1.99 (0.27), residues: 839 helix: -0.76 (0.24), residues: 389 sheet: -2.18 (0.59), residues: 76 loop : -1.63 (0.30), 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 0.018 0.002 PHE A 643 TYR 0.018 0.002 TYR A 820 ARG 0.004 0.001 ARG A 630 *********************** 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 123 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.5215 (mtm110) cc_final: 0.4307 (mmt180) REVERT: A 765 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.4991 (mm) REVERT: A 789 MET cc_start: 0.5794 (ttt) cc_final: 0.5542 (mtp) REVERT: A 820 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.4231 (p90) outliers start: 27 outliers final: 13 residues processed: 113 average time/residue: 0.1718 time to fit residues: 26.9053 Evaluate side-chains 103 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 192 THR 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 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: 1.9990 chunk 5 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 HIS ** 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 = 0.4794 r_free = 0.4794 target = 0.229368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.207072 restraints weight = 8663.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.211369 restraints weight = 5554.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.214432 restraints weight = 3874.912| |-----------------------------------------------------------------------------| r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5399 moved from start: 0.4625 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= 0.237 Angle : 1.039 31.381 9049 Z= 0.441 Chirality : 0.091 2.394 1039 Planarity : 0.005 0.058 1180 Dihedral : 10.381 127.287 976 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.07 % Allowed : 19.58 % Favored : 76.36 % 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: -1.77 (0.27), residues: 839 helix: -0.50 (0.24), residues: 395 sheet: -2.25 (0.58), residues: 78 loop : -1.57 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 166 HIS 0.015 0.002 HIS A 799 PHE 0.015 0.002 PHE A 640 TYR 0.022 0.002 TYR A 269 ARG 0.004 0.000 ARG A 63 *********************** 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 124 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.5450 (mtm110) cc_final: 0.4344 (mmt180) REVERT: A 464 ASN cc_start: 0.6068 (m-40) cc_final: 0.5378 (t0) REVERT: A 786 ILE cc_start: 0.6531 (pt) cc_final: 0.5777 (mp) REVERT: A 789 MET cc_start: 0.5779 (ttt) cc_final: 0.5565 (mtp) REVERT: A 820 TYR cc_start: 0.6417 (OUTLIER) cc_final: 0.4154 (p90) outliers start: 27 outliers final: 14 residues processed: 116 average time/residue: 0.1680 time to fit residues: 27.7010 Evaluate side-chains 101 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 807 LEU 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: 0.5980 chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4893 r_free = 0.4893 target = 0.238311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.222581 restraints weight = 8263.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.225207 restraints weight = 6438.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.226816 restraints weight = 4800.641| |-----------------------------------------------------------------------------| r_work (final): 0.4766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 moved from start: 0.5051 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= 0.254 Angle : 1.046 31.076 9049 Z= 0.440 Chirality : 0.090 2.394 1039 Planarity : 0.005 0.062 1180 Dihedral : 10.281 124.996 976 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.67 % Allowed : 20.33 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.27), residues: 839 helix: -0.58 (0.24), residues: 400 sheet: -2.25 (0.57), residues: 84 loop : -1.68 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 166 HIS 0.006 0.002 HIS A 759 PHE 0.017 0.002 PHE A 711 TYR 0.019 0.002 TYR A 269 ARG 0.009 0.001 ARG A 670 *********************** 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 126 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 ASN cc_start: 0.5945 (m-40) cc_final: 0.5325 (t0) REVERT: A 820 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.4552 (p90) outliers start: 31 outliers final: 20 residues processed: 113 average time/residue: 0.1520 time to fit residues: 24.4800 Evaluate side-chains 105 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 GLU 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 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 640 PHE Chi-restraints excluded: chain A residue 641 ILE 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: 0.7980 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 0.0000 chunk 75 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 0.1980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.225695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.203326 restraints weight = 8541.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.207628 restraints weight = 5439.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.210757 restraints weight = 3786.811| |-----------------------------------------------------------------------------| r_work (final): 0.4643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 moved from start: 0.5420 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= 0.244 Angle : 1.027 31.443 9049 Z= 0.428 Chirality : 0.089 2.380 1039 Planarity : 0.005 0.064 1180 Dihedral : 10.016 121.834 976 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.37 % Allowed : 21.23 % Favored : 74.40 % 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: -1.85 (0.27), residues: 839 helix: -0.50 (0.24), residues: 396 sheet: -2.15 (0.60), residues: 76 loop : -1.75 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 166 HIS 0.006 0.001 HIS A 759 PHE 0.011 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 122 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.6221 (m-80) cc_final: 0.5913 (m-80) REVERT: A 464 ASN cc_start: 0.5912 (m-40) cc_final: 0.5278 (t0) REVERT: A 669 ARG cc_start: 0.4626 (mtt90) cc_final: 0.4339 (mtt90) REVERT: A 820 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.4117 (p90) outliers start: 29 outliers final: 18 residues processed: 113 average time/residue: 0.1593 time to fit residues: 25.4272 Evaluate side-chains 104 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 191 GLU 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 370 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 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: 0.9990 chunk 46 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4767 r_free = 0.4767 target = 0.225265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.203692 restraints weight = 8539.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.207880 restraints weight = 5440.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.210923 restraints weight = 3770.774| |-----------------------------------------------------------------------------| r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6659 Z= 0.249 Angle : 1.038 31.178 9049 Z= 0.435 Chirality : 0.089 2.388 1039 Planarity : 0.005 0.062 1180 Dihedral : 9.926 120.365 976 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.07 % Allowed : 22.59 % Favored : 73.34 % 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: -1.76 (0.27), residues: 839 helix: -0.50 (0.24), residues: 390 sheet: -2.19 (0.59), residues: 76 loop : -1.58 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 166 HIS 0.006 0.001 HIS A 759 PHE 0.026 0.002 PHE A 643 TYR 0.017 0.001 TYR A 820 ARG 0.003 0.000 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 119 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.3352 (mtt) cc_final: 0.2843 (mtp) REVERT: A 412 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7460 (pt) REVERT: A 464 ASN cc_start: 0.5714 (m-40) cc_final: 0.5314 (t0) REVERT: A 726 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7336 (mp0) REVERT: A 765 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5691 (mm) REVERT: A 820 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.4090 (p90) REVERT: A 865 MET cc_start: 0.3067 (mmt) cc_final: 0.2793 (tpp) outliers start: 27 outliers final: 20 residues processed: 108 average time/residue: 0.1778 time to fit residues: 27.4406 Evaluate side-chains 106 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 191 GLU 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 370 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 412 LEU 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 765 LEU 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: 8.9990 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4745 r_free = 0.4745 target = 0.223212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.200996 restraints weight = 8691.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.205137 restraints weight = 5570.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.208234 restraints weight = 3905.723| |-----------------------------------------------------------------------------| r_work (final): 0.4607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.5870 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= 0.290 Angle : 1.059 31.436 9049 Z= 0.449 Chirality : 0.089 2.379 1039 Planarity : 0.005 0.059 1180 Dihedral : 9.983 119.981 976 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -1.78 (0.28), residues: 839 helix: -0.51 (0.24), residues: 390 sheet: -2.24 (0.61), residues: 76 loop : -1.60 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.006 0.002 HIS A 521 PHE 0.020 0.002 PHE A 643 TYR 0.032 0.002 TYR A 97 ARG 0.005 0.001 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 120 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.3486 (mtt) cc_final: 0.2897 (mtp) REVERT: A 412 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7549 (pt) REVERT: A 464 ASN cc_start: 0.5842 (m-40) cc_final: 0.5401 (t0) REVERT: A 726 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7278 (mp0) REVERT: A 765 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5736 (mm) REVERT: A 820 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.4333 (p90) REVERT: A 865 MET cc_start: 0.2688 (mmt) cc_final: 0.2298 (tpp) outliers start: 27 outliers final: 18 residues processed: 107 average time/residue: 0.1495 time to fit residues: 22.9958 Evaluate side-chains 109 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 191 GLU 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 370 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 412 LEU 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 765 LEU 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: 0.0980 chunk 73 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.225681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.203769 restraints weight = 8757.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.207956 restraints weight = 5612.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.211049 restraints weight = 3925.016| |-----------------------------------------------------------------------------| r_work (final): 0.4631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 moved from start: 0.6064 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= 0.231 Angle : 1.020 31.166 9049 Z= 0.427 Chirality : 0.089 2.394 1039 Planarity : 0.005 0.079 1180 Dihedral : 9.738 116.163 976 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.61 % Allowed : 23.64 % Favored : 72.74 % 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: -1.64 (0.28), residues: 839 helix: -0.42 (0.25), residues: 391 sheet: -2.26 (0.61), residues: 70 loop : -1.49 (0.31), residues: 378 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 0.021 0.002 PHE A 643 TYR 0.024 0.002 TYR A 97 ARG 0.007 0.000 ARG A 669 *********************** 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: 24 poor density : 92 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.3513 (mtt) cc_final: 0.2938 (mtp) REVERT: A 412 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7627 (pt) REVERT: A 464 ASN cc_start: 0.5861 (m-40) cc_final: 0.5378 (t0) REVERT: A 669 ARG cc_start: 0.4491 (mtt90) cc_final: 0.4216 (ttp-170) REVERT: A 726 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 765 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5463 (mm) REVERT: A 820 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.4024 (p90) REVERT: A 865 MET cc_start: 0.2417 (mmt) cc_final: 0.2081 (tpp) outliers start: 24 outliers final: 18 residues processed: 107 average time/residue: 0.1598 time to fit residues: 24.0090 Evaluate side-chains 108 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR 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 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 412 LEU 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 765 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: 0.4980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 79 optimal weight: 0.0040 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.224672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.202887 restraints weight = 8903.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.206965 restraints weight = 5712.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.210016 restraints weight = 3987.718| |-----------------------------------------------------------------------------| r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5447 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6659 Z= 0.241 Angle : 1.035 31.214 9049 Z= 0.434 Chirality : 0.089 2.391 1039 Planarity : 0.005 0.075 1180 Dihedral : 9.731 115.047 976 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.46 % Allowed : 24.10 % Favored : 72.44 % 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: -0.46 (0.24), residues: 403 sheet: -2.25 (0.60), residues: 75 loop : -1.52 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 166 HIS 0.007 0.002 HIS A 521 PHE 0.020 0.002 PHE A 643 TYR 0.021 0.002 TYR A 97 ARG 0.004 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 110 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.7173 (tp) cc_final: 0.6836 (pp) REVERT: A 210 MET cc_start: 0.3234 (mtt) cc_final: 0.2647 (mtp) REVERT: A 412 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7636 (pt) REVERT: A 464 ASN cc_start: 0.5728 (m-40) cc_final: 0.5421 (t0) REVERT: A 610 LEU cc_start: 0.5903 (pt) cc_final: 0.5440 (mt) REVERT: A 669 ARG cc_start: 0.4595 (mtt90) cc_final: 0.3876 (ttm170) REVERT: A 726 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 765 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5342 (mm) REVERT: A 814 MET cc_start: 0.4037 (tpt) cc_final: 0.3700 (tpt) REVERT: A 820 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.3938 (p90) REVERT: A 865 MET cc_start: 0.2326 (mmt) cc_final: 0.1966 (tpp) outliers start: 23 outliers final: 20 residues processed: 100 average time/residue: 0.1419 time to fit residues: 20.7855 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 : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 191 GLU 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 368 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 412 LEU 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 765 LEU 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: 0.5980 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4730 r_free = 0.4730 target = 0.222110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.200104 restraints weight = 8937.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.204110 restraints weight = 5740.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.207065 restraints weight = 4064.756| |-----------------------------------------------------------------------------| r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 moved from start: 0.6329 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= 0.272 Angle : 1.053 31.473 9049 Z= 0.444 Chirality : 0.089 2.379 1039 Planarity : 0.005 0.059 1180 Dihedral : 9.772 112.863 976 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.77 % Allowed : 23.80 % Favored : 72.44 % 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: -1.68 (0.28), residues: 839 helix: -0.54 (0.24), residues: 402 sheet: -2.36 (0.62), residues: 73 loop : -1.38 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 166 HIS 0.008 0.002 HIS A 521 PHE 0.019 0.002 PHE A 643 TYR 0.024 0.002 TYR A 97 ARG 0.005 0.001 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.48 seconds wall clock time: 42 minutes 23.68 seconds (2543.68 seconds total)