Starting phenix.real_space_refine on Wed Aug 5 17:34:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hzg_52524/08_2026/9hzg_52524_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hzg_52524/08_2026/9hzg_52524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hzg_52524/08_2026/9hzg_52524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hzg_52524/08_2026/9hzg_52524.map" model { file = "/net/cci-nas-00/data/ceres_data/9hzg_52524/08_2026/9hzg_52524_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hzg_52524/08_2026/9hzg_52524_trim.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 1 5.21 5 S 51 5.16 5 C 6680 2.51 5 N 1776 2.21 5 O 2013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10561 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4136 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 29, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 21, 'ASP:plan': 9, 'ARG:plan': 10, 'GLN:plan1': 3, 'PHE:plan': 1, 'HIS:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 203 Chain: "E" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1603 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 6, 'ASP:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4085 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 9, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "O" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "P" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.31, per 1000 atoms: 0.22 Number of scatterers: 10561 At special positions: 0 Unit cell: (93.888, 100.408, 135.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 40 15.00 Mg 1 11.99 O 2013 8.00 N 1776 7.00 C 6680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 305.2 milliseconds 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2482 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 40.2% alpha, 16.4% beta 7 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 179 through 196 Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.569A pdb=" N LEU A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.639A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.676A pdb=" N LYS A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A 462 " --> pdb=" O GLN A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'A' and resid 577 through 588 removed outlier: 3.906A pdb=" N GLU A 583 " --> pdb=" O PRO A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 609 Processing helix chain 'E' and resid 16 through 25 removed outlier: 3.866A pdb=" N GLN E 22 " --> pdb=" O TRP E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 40 through 44 removed outlier: 3.941A pdb=" N LEU E 44 " --> pdb=" O GLU E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 73 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 139 through 152 Processing helix chain 'E' and resid 161 through 170 removed outlier: 3.695A pdb=" N ASN E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 182 removed outlier: 4.005A pdb=" N LYS E 182 " --> pdb=" O ASN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 206 through 230 removed outlier: 3.525A pdb=" N ILE E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.824A pdb=" N ARG B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.797A pdb=" N GLU B 241 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.987A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.729A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 103 removed outlier: 7.514A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TYR A 88 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 42 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER A 37 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.637A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA A 395 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A 350 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 300 Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.589A pdb=" N PHE A 303 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 290 " --> pdb=" O PHE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.332A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 52 through 56 removed outlier: 5.933A pdb=" N SER E 52 " --> pdb=" O CYS E 109 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU E 111 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL E 54 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS E 113 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER E 56 " --> pdb=" O HIS E 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 99 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP E 82 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS E 135 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.530A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 8 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ALA B 55 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 10 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL B 57 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B 12 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE B 59 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET B 14 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 248 through 251 removed outlier: 6.521A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA B 396 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 464 through 466 446 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3117 1.33 - 1.45: 1589 1.45 - 1.57: 5984 1.57 - 1.69: 72 1.69 - 1.81: 82 Bond restraints: 10844 Sorted by residual: bond pdb=" C1' DT O 6 " pdb=" N1 DT O 6 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" C3' DC P 19 " pdb=" C2' DC P 19 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DT P 18 " pdb=" C2' DT P 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C1' DT O 3 " pdb=" N1 DT O 3 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DA P 17 " pdb=" C2' DA P 17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.64e+00 ... (remaining 10839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 14534 1.78 - 3.56: 300 3.56 - 5.34: 27 5.34 - 7.13: 5 7.13 - 8.91: 6 Bond angle restraints: 14872 Sorted by residual: angle pdb=" O4' DC P 27 " pdb=" C4' DC P 27 " pdb=" C3' DC P 27 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT P 20 " pdb=" C4 DT P 20 " pdb=" O4 DT P 20 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT O 13 " pdb=" C4 DT O 13 " pdb=" O4 DT O 13 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT P 18 " pdb=" C4 DT P 18 " pdb=" O4 DT P 18 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT O 6 " pdb=" C4 DT O 6 " pdb=" O4 DT O 6 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 14867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 6135 34.38 - 68.76: 335 68.76 - 103.14: 24 103.14 - 137.52: 2 137.52 - 171.90: 6 Dihedral angle restraints: 6502 sinusoidal: 2690 harmonic: 3812 Sorted by residual: dihedral pdb=" CA SER B 214 " pdb=" C SER B 214 " pdb=" N LEU B 215 " pdb=" CA LEU B 215 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLU B 328 " pdb=" C GLU B 328 " pdb=" N GLU B 329 " pdb=" CA GLU B 329 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" C4' DC P 19 " pdb=" C3' DC P 19 " pdb=" O3' DC P 19 " pdb=" P DT P 20 " ideal model delta sinusoidal sigma weight residual 220.00 48.10 171.90 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1289 0.038 - 0.076: 301 0.076 - 0.113: 116 0.113 - 0.151: 15 0.151 - 0.189: 2 Chirality restraints: 1723 Sorted by residual: chirality pdb=" C1 IHP A 701 " pdb=" C2 IHP A 701 " pdb=" C6 IHP A 701 " pdb=" O11 IHP A 701 " both_signs ideal model delta sigma weight residual False 2.32 2.50 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" C3 IHP A 701 " pdb=" C2 IHP A 701 " pdb=" C4 IHP A 701 " pdb=" O13 IHP A 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.50 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ILE B 24 " pdb=" N ILE B 24 " pdb=" C ILE B 24 " pdb=" CB ILE B 24 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1720 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 312 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 313 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 216 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLU B 216 " 0.022 2.00e-02 2.50e+03 pdb=" O GLU B 216 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY B 217 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 43 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C ASP E 43 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP E 43 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU E 44 " 0.007 2.00e-02 2.50e+03 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 326 2.68 - 3.24: 10826 3.24 - 3.79: 16024 3.79 - 4.35: 20512 4.35 - 4.90: 34534 Nonbonded interactions: 82222 Sorted by model distance: nonbonded pdb=" OG SER B 255 " pdb=" OD1 ASN B 256 " model vdw 2.127 3.040 nonbonded pdb=" O LYS B 286 " pdb=" NZ LYS B 286 " model vdw 2.133 3.120 nonbonded pdb=" N GLU B 428 " pdb=" OE1 GLU B 428 " model vdw 2.165 3.120 nonbonded pdb=" N GLU A 457 " pdb=" OE1 GLU A 457 " model vdw 2.183 3.120 nonbonded pdb=" NE2 GLN A 426 " pdb=" O PHE B 435 " model vdw 2.199 3.120 ... (remaining 82217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.790 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.004 0.052 10844 Z= 0.254 Angle : 0.572 8.907 14872 Z= 0.369 Chirality : 0.039 0.189 1723 Planarity : 0.002 0.034 1783 Dihedral : 20.510 171.903 4020 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 31.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.35 % Favored : 94.34 % Rotamer: Outliers : 0.30 % Allowed : 31.24 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1290 helix: 2.39 (0.26), residues: 461 sheet: 0.52 (0.39), residues: 187 loop : -0.20 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 196 TYR 0.010 0.001 TYR B 444 PHE 0.006 0.001 PHE B 59 TRP 0.004 0.001 TRP E 200 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.25 (10844) covalent geometry : angle 0.57153 / 0.37 (14872) hydrogen bonds : bond 0.16273 / 11.30 ( 461) hydrogen bonds : angle 7.30536 / 5.33 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 0.281 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 164 average time/residue: 0.0777 time to fit residues: 19.0893 Evaluate side-chains 154 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.126942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097088 restraints weight = 20424.977| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.12 r_work: 0.3065 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10844 Z= 0.160 Angle : 0.683 8.722 14872 Z= 0.360 Chirality : 0.047 0.339 1723 Planarity : 0.004 0.055 1783 Dihedral : 18.985 173.253 1804 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.57 % Rotamer: Outliers : 3.64 % Allowed : 26.29 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.24), residues: 1290 helix: 1.90 (0.25), residues: 469 sheet: 0.39 (0.37), residues: 196 loop : -0.22 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 431 TYR 0.014 0.002 TYR E 110 PHE 0.020 0.002 PHE B 59 TRP 0.008 0.001 TRP E 18 HIS 0.004 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (10844) covalent geometry : angle 0.68261 / 0.36 (14872) hydrogen bonds : bond 0.04299 / 2.97 ( 461) hydrogen bonds : angle 5.85549 / 4.29 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.284 Fit side-chains REVERT: A 426 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8553 (tt0) outliers start: 36 outliers final: 19 residues processed: 207 average time/residue: 0.0791 time to fit residues: 24.3314 Evaluate side-chains 193 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 533 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 127 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 61 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 ASN E 23 ASN B 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.131088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097908 restraints weight = 21520.894| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.31 r_work: 0.2976 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10844 Z= 0.144 Angle : 0.617 7.980 14872 Z= 0.328 Chirality : 0.045 0.347 1723 Planarity : 0.003 0.058 1783 Dihedral : 19.005 177.578 1803 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 4.04 % Allowed : 26.69 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1290 helix: 1.84 (0.25), residues: 468 sheet: 0.32 (0.37), residues: 196 loop : -0.24 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 130 TYR 0.011 0.001 TYR A 141 PHE 0.015 0.001 PHE E 81 TRP 0.009 0.001 TRP E 18 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (10844) covalent geometry : angle 0.61725 / 0.33 (14872) hydrogen bonds : bond 0.04032 / 2.80 ( 461) hydrogen bonds : angle 5.52283 / 4.06 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.345 Fit side-chains REVERT: E 157 ASN cc_start: 0.9253 (t0) cc_final: 0.8821 (t0) REVERT: B 116 ASP cc_start: 0.9374 (t70) cc_final: 0.9136 (t0) REVERT: B 225 TYR cc_start: 0.8903 (m-80) cc_final: 0.8647 (m-80) outliers start: 40 outliers final: 24 residues processed: 204 average time/residue: 0.0771 time to fit residues: 23.5264 Evaluate side-chains 196 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 533 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS E 23 ASN B 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.131318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097581 restraints weight = 21735.730| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.31 r_work: 0.3064 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10844 Z= 0.193 Angle : 0.624 7.930 14872 Z= 0.332 Chirality : 0.045 0.341 1723 Planarity : 0.004 0.060 1783 Dihedral : 18.949 178.073 1803 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.96 % Favored : 94.81 % Rotamer: Outliers : 4.25 % Allowed : 25.88 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.24), residues: 1290 helix: 1.70 (0.25), residues: 469 sheet: 0.17 (0.37), residues: 196 loop : -0.33 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 470 TYR 0.010 0.002 TYR A 217 PHE 0.016 0.001 PHE B 183 TRP 0.009 0.001 TRP E 18 HIS 0.004 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (10844) covalent geometry : angle 0.62409 / 0.33 (14872) hydrogen bonds : bond 0.03973 / 2.76 ( 461) hydrogen bonds : angle 5.39180 / 3.97 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.435 Fit side-chains REVERT: E 157 ASN cc_start: 0.9280 (t0) cc_final: 0.8891 (t0) REVERT: B 116 ASP cc_start: 0.9368 (t70) cc_final: 0.9121 (t0) REVERT: B 225 TYR cc_start: 0.8957 (m-80) cc_final: 0.8752 (m-80) outliers start: 42 outliers final: 36 residues processed: 201 average time/residue: 0.0785 time to fit residues: 23.9259 Evaluate side-chains 210 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 127 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS E 23 ASN B 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093539 restraints weight = 20426.516| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.20 r_work: 0.3140 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10844 Z= 0.134 Angle : 0.596 9.437 14872 Z= 0.315 Chirality : 0.044 0.335 1723 Planarity : 0.003 0.060 1783 Dihedral : 18.848 177.441 1803 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 4.04 % Allowed : 26.69 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1290 helix: 1.73 (0.25), residues: 469 sheet: 0.20 (0.38), residues: 189 loop : -0.33 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.016 0.001 TYR E 224 PHE 0.016 0.001 PHE B 59 TRP 0.008 0.001 TRP E 18 HIS 0.002 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10844) covalent geometry : angle 0.59567 / 0.32 (14872) hydrogen bonds : bond 0.03648 / 2.53 ( 461) hydrogen bonds : angle 5.18608 / 3.80 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.442 Fit side-chains REVERT: A 135 MET cc_start: 0.7933 (mmt) cc_final: 0.7366 (mmt) REVERT: A 219 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8655 (p0) REVERT: E 157 ASN cc_start: 0.9265 (t0) cc_final: 0.8859 (t0) REVERT: B 116 ASP cc_start: 0.9342 (t70) cc_final: 0.9089 (t0) REVERT: B 223 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8417 (mm-30) REVERT: B 225 TYR cc_start: 0.8859 (m-80) cc_final: 0.8512 (m-80) outliers start: 40 outliers final: 31 residues processed: 215 average time/residue: 0.0902 time to fit residues: 28.9368 Evaluate side-chains 209 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.0980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS E 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.098285 restraints weight = 21807.813| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.35 r_work: 0.3079 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10844 Z= 0.161 Angle : 0.598 8.301 14872 Z= 0.316 Chirality : 0.044 0.337 1723 Planarity : 0.004 0.060 1783 Dihedral : 18.801 177.620 1803 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 4.45 % Allowed : 27.00 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.24), residues: 1290 helix: 1.74 (0.25), residues: 468 sheet: 0.15 (0.37), residues: 189 loop : -0.33 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.012 0.001 TYR E 89 PHE 0.023 0.001 PHE E 81 TRP 0.009 0.001 TRP E 18 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (10844) covalent geometry : angle 0.59795 / 0.32 (14872) hydrogen bonds : bond 0.03701 / 2.57 ( 461) hydrogen bonds : angle 5.07512 / 3.73 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.354 Fit side-chains REVERT: A 135 MET cc_start: 0.8018 (mmt) cc_final: 0.7534 (mmt) REVERT: A 219 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8673 (p0) REVERT: E 157 ASN cc_start: 0.9253 (t0) cc_final: 0.8822 (t0) REVERT: B 116 ASP cc_start: 0.9349 (t70) cc_final: 0.9097 (t0) REVERT: B 223 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8517 (mm-30) REVERT: B 225 TYR cc_start: 0.8940 (m-80) cc_final: 0.8573 (m-80) outliers start: 44 outliers final: 35 residues processed: 204 average time/residue: 0.0810 time to fit residues: 24.7403 Evaluate side-chains 211 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 126 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 41 optimal weight: 0.0970 chunk 116 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.132529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099528 restraints weight = 21512.606| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.32 r_work: 0.3146 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10844 Z= 0.122 Angle : 0.590 8.571 14872 Z= 0.310 Chirality : 0.044 0.331 1723 Planarity : 0.004 0.061 1783 Dihedral : 18.648 174.817 1803 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 3.84 % Allowed : 27.91 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1290 helix: 1.76 (0.25), residues: 469 sheet: 0.24 (0.38), residues: 189 loop : -0.30 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 353 TYR 0.009 0.001 TYR E 89 PHE 0.029 0.001 PHE E 81 TRP 0.006 0.001 TRP E 18 HIS 0.002 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (10844) covalent geometry : angle 0.58955 / 0.31 (14872) hydrogen bonds : bond 0.03456 / 2.38 ( 461) hydrogen bonds : angle 4.96182 / 3.64 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.430 Fit side-chains REVERT: A 135 MET cc_start: 0.8015 (mmt) cc_final: 0.7481 (mmt) REVERT: A 219 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8650 (p0) REVERT: E 157 ASN cc_start: 0.9260 (t0) cc_final: 0.8825 (t0) REVERT: B 223 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8626 (mm-30) outliers start: 38 outliers final: 30 residues processed: 208 average time/residue: 0.0819 time to fit residues: 25.7908 Evaluate side-chains 209 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 62 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.131853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098611 restraints weight = 21313.969| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.29 r_work: 0.3140 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10844 Z= 0.137 Angle : 0.592 9.096 14872 Z= 0.311 Chirality : 0.044 0.335 1723 Planarity : 0.004 0.060 1783 Dihedral : 18.622 176.330 1803 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 3.74 % Allowed : 28.31 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1290 helix: 1.73 (0.25), residues: 469 sheet: 0.28 (0.37), residues: 190 loop : -0.28 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 353 TYR 0.016 0.001 TYR E 224 PHE 0.024 0.001 PHE E 81 TRP 0.007 0.001 TRP E 18 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10844) covalent geometry : angle 0.59165 / 0.31 (14872) hydrogen bonds : bond 0.03512 / 2.43 ( 461) hydrogen bonds : angle 4.88918 / 3.58 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.461 Fit side-chains REVERT: A 135 MET cc_start: 0.8034 (mmt) cc_final: 0.7571 (mmt) REVERT: A 219 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8662 (p0) REVERT: E 157 ASN cc_start: 0.9245 (t0) cc_final: 0.8807 (t0) REVERT: B 223 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8449 (mm-30) REVERT: B 225 TYR cc_start: 0.8898 (m-80) cc_final: 0.8505 (m-80) REVERT: B 427 MET cc_start: 0.9178 (ttp) cc_final: 0.8894 (ptp) outliers start: 37 outliers final: 32 residues processed: 199 average time/residue: 0.0824 time to fit residues: 24.3946 Evaluate side-chains 205 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 34 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN E 23 ASN E 188 GLN B 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096935 restraints weight = 21606.183| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.29 r_work: 0.3066 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10844 Z= 0.193 Angle : 0.623 8.855 14872 Z= 0.327 Chirality : 0.045 0.332 1723 Planarity : 0.004 0.060 1783 Dihedral : 18.630 176.601 1803 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.12 % Favored : 94.65 % Rotamer: Outliers : 3.94 % Allowed : 28.51 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1290 helix: 1.66 (0.25), residues: 469 sheet: 0.10 (0.37), residues: 192 loop : -0.29 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 353 TYR 0.026 0.002 TYR E 110 PHE 0.031 0.001 PHE E 81 TRP 0.008 0.001 TRP E 18 HIS 0.004 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (10844) covalent geometry : angle 0.62269 / 0.33 (14872) hydrogen bonds : bond 0.03862 / 2.68 ( 461) hydrogen bonds : angle 4.91573 / 3.59 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.379 Fit side-chains REVERT: A 135 MET cc_start: 0.8118 (mmt) cc_final: 0.7717 (mmt) REVERT: A 219 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8689 (p0) REVERT: A 409 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.8845 (t80) REVERT: E 103 CYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7688 (m) REVERT: E 157 ASN cc_start: 0.9232 (t0) cc_final: 0.8779 (t0) REVERT: B 183 PHE cc_start: 0.8274 (t80) cc_final: 0.8034 (t80) REVERT: B 223 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8599 (mm-30) REVERT: B 225 TYR cc_start: 0.8991 (m-80) cc_final: 0.8597 (m-80) outliers start: 39 outliers final: 29 residues processed: 193 average time/residue: 0.0794 time to fit residues: 23.3287 Evaluate side-chains 199 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 19 optimal weight: 0.0980 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.122180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092670 restraints weight = 20629.224| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.19 r_work: 0.3132 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10844 Z= 0.154 Angle : 0.613 9.509 14872 Z= 0.320 Chirality : 0.044 0.328 1723 Planarity : 0.004 0.060 1783 Dihedral : 18.591 176.864 1803 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 3.24 % Allowed : 29.02 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1290 helix: 1.66 (0.25), residues: 469 sheet: 0.18 (0.37), residues: 190 loop : -0.31 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.020 0.001 TYR E 110 PHE 0.032 0.001 PHE E 81 TRP 0.010 0.001 TRP E 18 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (10844) covalent geometry : angle 0.61287 / 0.32 (14872) hydrogen bonds : bond 0.03672 / 2.54 ( 461) hydrogen bonds : angle 4.89762 / 3.59 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.390 Fit side-chains REVERT: A 135 MET cc_start: 0.8078 (mmt) cc_final: 0.7610 (mmt) REVERT: A 219 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8659 (p0) REVERT: A 409 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8813 (t80) REVERT: E 103 CYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7645 (m) REVERT: E 157 ASN cc_start: 0.9227 (t0) cc_final: 0.8769 (t0) REVERT: E 224 TYR cc_start: 0.9129 (t80) cc_final: 0.8844 (t80) REVERT: B 183 PHE cc_start: 0.8275 (t80) cc_final: 0.8043 (t80) REVERT: B 223 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8531 (mm-30) REVERT: B 225 TYR cc_start: 0.8914 (m-80) cc_final: 0.8516 (m-80) outliers start: 32 outliers final: 28 residues processed: 191 average time/residue: 0.0787 time to fit residues: 22.8163 Evaluate side-chains 201 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 27 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 489 ASN E 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.130441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.101166 restraints weight = 20507.149| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.16 r_work: 0.3028 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10844 Z= 0.124 Angle : 0.603 9.184 14872 Z= 0.314 Chirality : 0.044 0.332 1723 Planarity : 0.004 0.060 1783 Dihedral : 18.484 178.682 1803 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 3.03 % Allowed : 29.52 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1290 helix: 1.70 (0.25), residues: 468 sheet: 0.17 (0.37), residues: 192 loop : -0.26 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.023 0.001 TYR E 110 PHE 0.035 0.001 PHE E 81 TRP 0.011 0.001 TRP E 18 HIS 0.002 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10844) covalent geometry : angle 0.60335 / 0.31 (14872) hydrogen bonds : bond 0.03414 / 2.34 ( 461) hydrogen bonds : angle 4.80894 / 3.52 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.84 seconds wall clock time: 37 minutes 19.06 seconds (2239.06 seconds total)