Starting phenix.real_space_refine on Thu Jul 2 22:56:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ouo_17197/07_2026/8ouo_17197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ouo_17197/07_2026/8ouo_17197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ouo_17197/07_2026/8ouo_17197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ouo_17197/07_2026/8ouo_17197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ouo_17197/07_2026/8ouo_17197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ouo_17197/07_2026/8ouo_17197.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.021 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 61 5.16 5 C 7224 2.51 5 N 1657 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10749 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5195 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 25, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5011 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 602} Chain breaks: 4 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 312 Unusual residues: {'PCF': 1, 'PLD': 1, 'Q7G': 2, 'W4E': 1, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 30 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 231 Unusual residues: {'PCF': 1, 'PLD': 1, 'Q7G': 1, 'Y01': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Time building chain proxies: 2.06, per 1000 atoms: 0.19 Number of scatterers: 10749 At special positions: 0 Unit cell: (105.283, 90.361, 115.231, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 4 15.00 O 1803 8.00 N 1657 7.00 C 7224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS B 623 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 180 " distance=2.03 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: 0.83 Conformation dependent library (CDL) restraints added in 347.8 milliseconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 37 through 58 Processing helix chain 'A' and resid 67 through 78 removed outlier: 4.039A pdb=" N TRP A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 96 Processing helix chain 'A' and resid 97 through 100 removed outlier: 3.712A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 100' Processing helix chain 'A' and resid 121 through 147 removed outlier: 4.572A pdb=" N THR A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 126 " --> pdb=" O CYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.760A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Proline residue: A 192 - end of helix removed outlier: 3.966A pdb=" N LEU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 273 through 285 removed outlier: 4.051A pdb=" N MET A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 287 through 299 removed outlier: 4.053A pdb=" N PHE A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 removed outlier: 3.713A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 343 removed outlier: 3.610A pdb=" N SER A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 419 through 431 Processing helix chain 'A' and resid 432 through 459 removed outlier: 3.522A pdb=" N ASP A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 492 Processing helix chain 'A' and resid 492 through 499 removed outlier: 4.092A pdb=" N TYR A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 524 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 558 through 561 Processing helix chain 'A' and resid 562 through 578 removed outlier: 4.078A pdb=" N VAL A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 601 removed outlier: 4.234A pdb=" N PHE A 582 " --> pdb=" O ASN A 578 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 651 Processing helix chain 'A' and resid 654 through 667 removed outlier: 3.744A pdb=" N PHE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 681 removed outlier: 4.248A pdb=" N TYR A 673 " --> pdb=" O TRP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 701 removed outlier: 3.711A pdb=" N ASN A 687 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 59 Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.638A pdb=" N TRP B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 Processing helix chain 'B' and resid 97 through 100 removed outlier: 3.785A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 100' Processing helix chain 'B' and resid 121 through 147 removed outlier: 4.587A pdb=" N THR B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU B 126 " --> pdb=" O CYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 155 through 178 Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.954A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 238 removed outlier: 3.608A pdb=" N LYS B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Proline residue: B 214 - end of helix removed outlier: 3.525A pdb=" N SER B 218 " --> pdb=" O PRO B 214 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 236 " --> pdb=" O MET B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.911A pdb=" N MET B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Proline residue: B 280 - end of helix removed outlier: 3.888A pdb=" N LYS B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 4.090A pdb=" N ILE B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 292 " --> pdb=" O TYR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.862A pdb=" N THR B 308 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 345 Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 372 through 387 Processing helix chain 'B' and resid 392 through 400 removed outlier: 3.739A pdb=" N PHE B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 418 through 431 removed outlier: 3.563A pdb=" N LEU B 422 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N SER B 424 " --> pdb=" O PRO B 420 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA B 425 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 456 removed outlier: 4.021A pdb=" N ASP B 435 " --> pdb=" O HIS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 492 Processing helix chain 'B' and resid 492 through 499 removed outlier: 4.341A pdb=" N TYR B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 523 Processing helix chain 'B' and resid 539 through 555 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.669A pdb=" N SER B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 578 removed outlier: 3.906A pdb=" N VAL B 568 " --> pdb=" O PRO B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 601 Processing helix chain 'B' and resid 630 through 634 removed outlier: 4.601A pdb=" N ALA B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.772A pdb=" N PHE B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 701 removed outlier: 3.710A pdb=" N ILE B 684 " --> pdb=" O VAL B 680 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU B 688 " --> pdb=" O ILE B 684 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 689 " --> pdb=" O TRP B 685 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2142 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: 1.36 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1555 1.32 - 1.44: 3089 1.44 - 1.57: 6292 1.57 - 1.69: 8 1.69 - 1.81: 102 Bond restraints: 11046 Sorted by residual: bond pdb=" C4 PLD B 801 " pdb=" O4P PLD B 801 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C4 PLD A 801 " pdb=" O4P PLD A 801 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" O13 PCF A 804 " pdb=" P PCF A 804 " ideal model delta sigma weight residual 1.653 1.606 0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" O13 PCF B 802 " pdb=" P PCF B 802 " ideal model delta sigma weight residual 1.653 1.606 0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C1 PLD A 801 " pdb=" O3P PLD A 801 " ideal model delta sigma weight residual 1.410 1.457 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 11041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 14882 2.15 - 4.29: 157 4.29 - 6.44: 27 6.44 - 8.59: 4 8.59 - 10.73: 3 Bond angle restraints: 15073 Sorted by residual: angle pdb=" O3P PLD B 801 " pdb=" P PLD B 801 " pdb=" O4P PLD B 801 " ideal model delta sigma weight residual 92.85 103.58 -10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C22 Q7G A 802 " pdb=" C23 Q7G A 802 " pdb=" C48 Q7G A 802 " ideal model delta sigma weight residual 117.02 106.95 10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O3P PLD A 801 " pdb=" P PLD A 801 " pdb=" O4P PLD A 801 " ideal model delta sigma weight residual 92.85 102.34 -9.49 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C2 W4E A 803 " pdb=" N1 W4E A 803 " pdb=" C4 W4E A 803 " ideal model delta sigma weight residual 116.97 109.87 7.10 3.00e+00 1.11e-01 5.60e+00 angle pdb=" C24 Q7G A 802 " pdb=" C23 Q7G A 802 " pdb=" C48 Q7G A 802 " ideal model delta sigma weight residual 107.24 113.97 -6.73 3.00e+00 1.11e-01 5.04e+00 ... (remaining 15068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.92: 6855 29.92 - 59.83: 178 59.83 - 89.75: 25 89.75 - 119.66: 13 119.66 - 149.58: 4 Dihedral angle restraints: 7075 sinusoidal: 3322 harmonic: 3753 Sorted by residual: dihedral pdb=" C1B PLD B 801 " pdb=" CB PLD B 801 " pdb=" O3 PLD B 801 " pdb=" C3 PLD B 801 " ideal model delta sinusoidal sigma weight residual 173.67 24.09 149.58 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" OB PLD B 801 " pdb=" CB PLD B 801 " pdb=" O3 PLD B 801 " pdb=" C3 PLD B 801 " ideal model delta sinusoidal sigma weight residual -7.40 -155.92 148.52 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" CA SER A 177 " pdb=" C SER A 177 " pdb=" N LEU A 178 " pdb=" CA LEU A 178 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 7072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1533 0.054 - 0.107: 212 0.107 - 0.161: 10 0.161 - 0.214: 2 0.214 - 0.268: 2 Chirality restraints: 1759 Sorted by residual: chirality pdb=" C2 PCF B 802 " pdb=" C1 PCF B 802 " pdb=" C3 PCF B 802 " pdb=" O21 PCF B 802 " both_signs ideal model delta sigma weight residual False -2.60 -2.33 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5C Q7G A 802 " pdb=" C4C Q7G A 802 " pdb=" C6C Q7G A 802 " pdb=" O5C Q7G A 802 " both_signs ideal model delta sigma weight residual False -2.50 -2.25 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C73 Q7G A 802 " pdb=" C74 Q7G A 802 " pdb=" C76 Q7G A 802 " pdb=" O80 Q7G A 802 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1756 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G A 802 " -0.021 2.00e-02 2.50e+03 1.05e-01 1.38e+02 pdb=" C13 Q7G A 802 " -0.030 2.00e-02 2.50e+03 pdb=" C14 Q7G A 802 " -0.170 2.00e-02 2.50e+03 pdb=" C15 Q7G A 802 " 0.127 2.00e-02 2.50e+03 pdb=" C16 Q7G A 802 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G A 808 " -0.018 2.00e-02 2.50e+03 8.91e-02 9.92e+01 pdb=" C13 Q7G A 808 " -0.028 2.00e-02 2.50e+03 pdb=" C14 Q7G A 808 " -0.143 2.00e-02 2.50e+03 pdb=" C15 Q7G A 808 " 0.107 2.00e-02 2.50e+03 pdb=" C16 Q7G A 808 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G B 806 " -0.010 2.00e-02 2.50e+03 5.25e-02 3.45e+01 pdb=" C13 Q7G B 806 " -0.019 2.00e-02 2.50e+03 pdb=" C14 Q7G B 806 " -0.083 2.00e-02 2.50e+03 pdb=" C15 Q7G B 806 " 0.063 2.00e-02 2.50e+03 pdb=" C16 Q7G B 806 " 0.049 2.00e-02 2.50e+03 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1847 2.76 - 3.30: 10749 3.30 - 3.83: 18182 3.83 - 4.37: 20854 4.37 - 4.90: 36448 Nonbonded interactions: 88080 Sorted by model distance: nonbonded pdb=" O SER A 104 " pdb=" OG SER A 104 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 631 " pdb=" OD1 ASP B 276 " model vdw 2.246 3.040 nonbonded pdb=" O SER B 104 " pdb=" OG SER B 104 " model vdw 2.249 3.040 nonbonded pdb=" O LEU A 366 " pdb=" NZ LYS A 376 " model vdw 2.267 3.120 nonbonded pdb=" O LYS A 382 " pdb=" OG SER A 385 " model vdw 2.271 3.040 ... (remaining 88075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 39 through 41 and (name N or name CA or name C or name O \ or name CB )) or resid 42 through 240 or (resid 251 and (name N or name CA or na \ me C or name O or name CB )) or resid 252 through 397 or (resid 398 and (name N \ or name CA or name C or name O or name CB )) or resid 399 through 408 or (resid \ 409 through 410 and (name N or name CA or name C or name O or name CB )) or resi \ d 411 through 422 or (resid 423 and (name N or name CA or name C or name O or na \ me CB )) or resid 424 through 463 or (resid 464 and (name N or name CA or name C \ or name O or name CB )) or resid 465 through 525 or (resid 537 and (name N or n \ ame CA or name C or name O or name CB )) or resid 538 through 801 or resid 805)) \ selection = (chain 'B' and (resid 39 through 344 or (resid 345 and (name N or name CA or nam \ e C or name O or name CB )) or resid 346 through 562 or (resid 563 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 564 through 699 \ or (resid 700 through 701 and (name N or name CA or name C or name O or name CB \ )) or (resid 801 and (name N or name CB or name OB or name C' or name C1 or name \ C1' or name C1B or name C2 or name C2' or name C2B or name C3 or name C3' or na \ me C3B or name C4 or name C4' or name C4B or name C5 or name C5' or name C5B or \ name C6 or name C6' or name C6B or name C7 or name C7' or name C7B or name C8 or \ name C8' or name C8B or name C9' or name CA' or name CB' or name O' or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4P or name P )) or resid \ 805)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.200 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:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.003 0.049 11049 Z= 0.165 Angle : 0.556 10.734 15079 Z= 0.254 Chirality : 0.037 0.268 1759 Planarity : 0.005 0.105 1769 Dihedral : 14.435 149.581 4634 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.53 % Allowed : 4.42 % Favored : 94.04 % 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: 2.07 (0.25), residues: 1257 helix: 2.00 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.43 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.011 0.001 TYR B 591 PHE 0.013 0.001 PHE A 626 TRP 0.009 0.001 TRP A 530 HIS 0.002 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (11046) covalent geometry : angle 0.55580 / 0.25 (15073) SS BOND : bond 0.00069 / 0.04 ( 3) SS BOND : angle 0.74618 / 0.42 ( 6) hydrogen bonds : bond 0.11473 / 7.45 ( 722) hydrogen bonds : angle 4.96092 / 3.66 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8235 (m110) cc_final: 0.7978 (m-40) REVERT: A 71 MET cc_start: 0.8243 (tpp) cc_final: 0.7834 (mpp) REVERT: A 76 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.7322 (mmm160) REVERT: A 80 ASN cc_start: 0.7920 (t0) cc_final: 0.7680 (t0) REVERT: A 161 TYR cc_start: 0.8343 (t80) cc_final: 0.7757 (t80) REVERT: A 339 GLU cc_start: 0.7951 (tt0) cc_final: 0.7487 (mm-30) REVERT: A 494 ARG cc_start: 0.8148 (ttt180) cc_final: 0.7848 (tpp-160) REVERT: A 524 ARG cc_start: 0.7519 (mmt-90) cc_final: 0.7026 (mmt-90) REVERT: A 562 MET cc_start: 0.7316 (ptm) cc_final: 0.7104 (ptm) REVERT: A 590 TYR cc_start: 0.8880 (m-80) cc_final: 0.8668 (m-80) REVERT: B 42 TRP cc_start: 0.7149 (t60) cc_final: 0.6887 (t60) REVERT: B 110 ASP cc_start: 0.8968 (m-30) cc_final: 0.8646 (m-30) REVERT: B 153 GLN cc_start: 0.7486 (tt0) cc_final: 0.7103 (tp-100) REVERT: B 232 MET cc_start: 0.8771 (mmt) cc_final: 0.8495 (mmt) REVERT: B 260 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7462 (mp0) REVERT: B 431 HIS cc_start: 0.8085 (t-90) cc_final: 0.7508 (t-90) REVERT: B 479 TYR cc_start: 0.8507 (t80) cc_final: 0.7645 (t80) REVERT: B 516 GLU cc_start: 0.8225 (tp30) cc_final: 0.7536 (tp30) REVERT: B 520 LEU cc_start: 0.8997 (tp) cc_final: 0.8674 (mp) REVERT: B 638 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8686 (p0) outliers start: 17 outliers final: 6 residues processed: 209 average time/residue: 0.3875 time to fit residues: 88.9728 Evaluate side-chains 120 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 623 CYS Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 693 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 HIS ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089918 restraints weight = 15165.379| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.20 r_work: 0.3020 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11049 Z= 0.172 Angle : 0.605 8.161 15079 Z= 0.292 Chirality : 0.039 0.152 1759 Planarity : 0.004 0.059 1769 Dihedral : 12.996 108.536 2349 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.16 % Allowed : 12.00 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.24), residues: 1257 helix: 2.06 (0.16), residues: 942 sheet: None (None), residues: 0 loop : -0.25 (0.39), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 384 TYR 0.017 0.001 TYR A 523 PHE 0.022 0.001 PHE B 452 TRP 0.013 0.001 TRP B 149 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (11046) covalent geometry : angle 0.60537 / 0.29 (15073) SS BOND : bond 0.00089 / 0.05 ( 3) SS BOND : angle 0.31813 / 0.15 ( 6) hydrogen bonds : bond 0.03902 / 2.61 ( 722) hydrogen bonds : angle 3.89286 / 2.89 ( 2142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.394 Fit side-chains REVERT: A 63 ASN cc_start: 0.8485 (m110) cc_final: 0.8056 (m110) REVERT: A 76 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.7420 (mmm160) REVERT: A 80 ASN cc_start: 0.7934 (t0) cc_final: 0.7700 (t0) REVERT: A 139 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7991 (t0) REVERT: A 339 GLU cc_start: 0.8101 (tt0) cc_final: 0.7576 (mm-30) REVERT: A 494 ARG cc_start: 0.8306 (ttt180) cc_final: 0.7880 (tpp-160) REVERT: A 524 ARG cc_start: 0.7466 (mmt-90) cc_final: 0.7013 (mmt-90) REVERT: B 42 TRP cc_start: 0.7308 (t60) cc_final: 0.6927 (t60) REVERT: B 110 ASP cc_start: 0.9025 (m-30) cc_final: 0.8794 (m-30) REVERT: B 153 GLN cc_start: 0.7623 (tt0) cc_final: 0.7264 (tm-30) REVERT: B 202 MET cc_start: 0.8560 (mtp) cc_final: 0.8111 (mtp) REVERT: B 260 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7805 (mp0) REVERT: B 431 HIS cc_start: 0.8229 (t-90) cc_final: 0.7641 (t-90) REVERT: B 445 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8361 (t0) REVERT: B 479 TYR cc_start: 0.8637 (t80) cc_final: 0.7731 (t80) REVERT: B 516 GLU cc_start: 0.8314 (tp30) cc_final: 0.7837 (tp30) REVERT: B 520 LEU cc_start: 0.8953 (tp) cc_final: 0.8712 (mp) REVERT: B 650 MET cc_start: 0.9278 (ttp) cc_final: 0.9032 (ttm) outliers start: 35 outliers final: 14 residues processed: 148 average time/residue: 0.3761 time to fit residues: 61.5412 Evaluate side-chains 123 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 623 CYS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 693 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 124 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092040 restraints weight = 15092.387| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.18 r_work: 0.3036 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11049 Z= 0.113 Angle : 0.526 6.774 15079 Z= 0.259 Chirality : 0.037 0.140 1759 Planarity : 0.004 0.063 1769 Dihedral : 11.363 88.907 2347 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.25 % Allowed : 12.73 % Favored : 84.03 % 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: 2.50 (0.24), residues: 1257 helix: 2.25 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -0.20 (0.39), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 384 TYR 0.013 0.001 TYR A 432 PHE 0.018 0.001 PHE A 626 TRP 0.015 0.001 TRP B 149 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (11046) covalent geometry : angle 0.52577 / 0.26 (15073) SS BOND : bond 0.00053 / 0.03 ( 3) SS BOND : angle 0.25376 / 0.16 ( 6) hydrogen bonds : bond 0.03503 / 2.33 ( 722) hydrogen bonds : angle 3.71961 / 2.77 ( 2142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.364 Fit side-chains REVERT: A 63 ASN cc_start: 0.8513 (m110) cc_final: 0.8083 (m110) REVERT: A 71 MET cc_start: 0.8174 (mpp) cc_final: 0.7773 (mpp) REVERT: A 76 ARG cc_start: 0.8111 (tpp-160) cc_final: 0.7351 (mmm160) REVERT: A 80 ASN cc_start: 0.7868 (t0) cc_final: 0.7644 (t0) REVERT: A 139 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7916 (t0) REVERT: A 339 GLU cc_start: 0.8106 (tt0) cc_final: 0.7604 (mm-30) REVERT: A 494 ARG cc_start: 0.8283 (ttt180) cc_final: 0.7855 (tpp-160) REVERT: A 524 ARG cc_start: 0.7388 (mmt-90) cc_final: 0.6981 (mmt-90) REVERT: A 579 MET cc_start: 0.6949 (ttm) cc_final: 0.6619 (ttp) REVERT: B 42 TRP cc_start: 0.7155 (t60) cc_final: 0.6905 (t60) REVERT: B 110 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8740 (m-30) REVERT: B 153 GLN cc_start: 0.7614 (tt0) cc_final: 0.7262 (tm-30) REVERT: B 260 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7753 (mp0) REVERT: B 405 ARG cc_start: 0.8665 (ppp80) cc_final: 0.8378 (ptm-80) REVERT: B 479 TYR cc_start: 0.8598 (t80) cc_final: 0.7725 (t80) REVERT: B 516 GLU cc_start: 0.8272 (tp30) cc_final: 0.7805 (tp30) outliers start: 36 outliers final: 13 residues processed: 151 average time/residue: 0.3656 time to fit residues: 61.1972 Evaluate side-chains 120 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 623 CYS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 693 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 66 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092907 restraints weight = 15229.086| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.20 r_work: 0.3066 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11049 Z= 0.113 Angle : 0.520 8.527 15079 Z= 0.256 Chirality : 0.037 0.138 1759 Planarity : 0.004 0.062 1769 Dihedral : 10.615 88.293 2345 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.71 % Allowed : 14.26 % Favored : 83.03 % 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: 2.52 (0.24), residues: 1257 helix: 2.29 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -0.27 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 384 TYR 0.015 0.001 TYR B 432 PHE 0.017 0.001 PHE A 626 TRP 0.016 0.001 TRP B 149 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (11046) covalent geometry : angle 0.52044 / 0.26 (15073) SS BOND : bond 0.00055 / 0.03 ( 3) SS BOND : angle 0.24001 / 0.15 ( 6) hydrogen bonds : bond 0.03330 / 2.22 ( 722) hydrogen bonds : angle 3.65997 / 2.73 ( 2142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.284 Fit side-chains REVERT: A 63 ASN cc_start: 0.8520 (m110) cc_final: 0.8089 (m110) REVERT: A 71 MET cc_start: 0.8288 (mpp) cc_final: 0.7752 (mpp) REVERT: A 76 ARG cc_start: 0.8132 (tpp-160) cc_final: 0.7386 (mmm160) REVERT: A 80 ASN cc_start: 0.7899 (t0) cc_final: 0.7673 (t0) REVERT: A 139 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7910 (t0) REVERT: A 339 GLU cc_start: 0.8136 (tt0) cc_final: 0.7628 (mm-30) REVERT: A 494 ARG cc_start: 0.8313 (ttt180) cc_final: 0.7906 (tpp-160) REVERT: A 524 ARG cc_start: 0.7484 (mmt-90) cc_final: 0.7096 (mmt-90) REVERT: A 579 MET cc_start: 0.6930 (ttm) cc_final: 0.6595 (ttp) REVERT: B 42 TRP cc_start: 0.7260 (t60) cc_final: 0.6904 (t60) REVERT: B 110 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8735 (m-30) REVERT: B 153 GLN cc_start: 0.7646 (tt0) cc_final: 0.7304 (tm-30) REVERT: B 202 MET cc_start: 0.8497 (mtp) cc_final: 0.8082 (mtp) REVERT: B 260 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7772 (mp0) REVERT: B 405 ARG cc_start: 0.8698 (ppp80) cc_final: 0.8397 (ptm-80) REVERT: B 431 HIS cc_start: 0.8156 (t-90) cc_final: 0.7514 (t-90) REVERT: B 479 TYR cc_start: 0.8627 (t80) cc_final: 0.7907 (t80) REVERT: B 516 GLU cc_start: 0.8337 (tp30) cc_final: 0.8082 (tp30) outliers start: 30 outliers final: 13 residues processed: 134 average time/residue: 0.4078 time to fit residues: 59.8145 Evaluate side-chains 118 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 623 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 0.0050 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 431 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 = 0.3590 r_free = 0.3590 target = 0.122351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.092268 restraints weight = 15185.728| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.19 r_work: 0.3058 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11049 Z= 0.114 Angle : 0.504 6.240 15079 Z= 0.252 Chirality : 0.037 0.138 1759 Planarity : 0.004 0.052 1769 Dihedral : 10.245 88.132 2342 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.44 % Allowed : 14.53 % Favored : 83.03 % 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: 2.51 (0.24), residues: 1257 helix: 2.32 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.37 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 384 TYR 0.010 0.001 TYR B 523 PHE 0.017 0.001 PHE A 626 TRP 0.018 0.001 TRP B 149 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (11046) covalent geometry : angle 0.50442 / 0.25 (15073) SS BOND : bond 0.00059 / 0.03 ( 3) SS BOND : angle 0.20794 / 0.12 ( 6) hydrogen bonds : bond 0.03297 / 2.18 ( 722) hydrogen bonds : angle 3.63495 / 2.72 ( 2142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.358 Fit side-chains REVERT: A 63 ASN cc_start: 0.8540 (m110) cc_final: 0.8107 (m110) REVERT: A 71 MET cc_start: 0.8277 (mpp) cc_final: 0.7763 (mpp) REVERT: A 76 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7405 (mmm160) REVERT: A 80 ASN cc_start: 0.7894 (t0) cc_final: 0.7670 (t0) REVERT: A 139 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7938 (t0) REVERT: A 339 GLU cc_start: 0.8144 (tt0) cc_final: 0.7641 (mm-30) REVERT: A 494 ARG cc_start: 0.8307 (ttt180) cc_final: 0.7886 (tpp-160) REVERT: A 524 ARG cc_start: 0.7429 (mmt-90) cc_final: 0.7072 (mmt-90) REVERT: A 579 MET cc_start: 0.6892 (ttm) cc_final: 0.6562 (ttp) REVERT: B 42 TRP cc_start: 0.7332 (t60) cc_final: 0.6934 (t60) REVERT: B 110 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8749 (m-30) REVERT: B 153 GLN cc_start: 0.7650 (tt0) cc_final: 0.7296 (tm-30) REVERT: B 260 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7787 (mp0) REVERT: B 405 ARG cc_start: 0.8699 (ppp80) cc_final: 0.8431 (ptm-80) REVERT: B 479 TYR cc_start: 0.8613 (t80) cc_final: 0.7857 (t80) REVERT: B 516 GLU cc_start: 0.8276 (tp30) cc_final: 0.8000 (tp30) REVERT: B 520 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8679 (mp) outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 0.4305 time to fit residues: 61.8180 Evaluate side-chains 118 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 623 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091311 restraints weight = 15253.629| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.20 r_work: 0.3046 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11049 Z= 0.132 Angle : 0.525 7.219 15079 Z= 0.261 Chirality : 0.037 0.143 1759 Planarity : 0.004 0.049 1769 Dihedral : 10.124 87.230 2342 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.98 % Allowed : 14.71 % Favored : 82.31 % 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: 2.52 (0.24), residues: 1257 helix: 2.33 (0.17), residues: 942 sheet: None (None), residues: 0 loop : -0.40 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 384 TYR 0.014 0.001 TYR B 432 PHE 0.018 0.001 PHE A 626 TRP 0.019 0.001 TRP B 149 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (11046) covalent geometry : angle 0.52461 / 0.26 (15073) SS BOND : bond 0.00088 / 0.05 ( 3) SS BOND : angle 0.27346 / 0.14 ( 6) hydrogen bonds : bond 0.03359 / 2.22 ( 722) hydrogen bonds : angle 3.64875 / 2.74 ( 2142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.282 Fit side-chains REVERT: A 63 ASN cc_start: 0.8535 (m110) cc_final: 0.8099 (m110) REVERT: A 76 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7390 (mmm160) REVERT: A 80 ASN cc_start: 0.7916 (t0) cc_final: 0.7687 (t0) REVERT: A 139 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7975 (t0) REVERT: A 202 MET cc_start: 0.8380 (mtm) cc_final: 0.8067 (mtp) REVERT: A 339 GLU cc_start: 0.8162 (tt0) cc_final: 0.7664 (mm-30) REVERT: A 494 ARG cc_start: 0.8311 (ttt180) cc_final: 0.7899 (tpp-160) REVERT: A 524 ARG cc_start: 0.7431 (mmt-90) cc_final: 0.7135 (mmt-90) REVERT: A 579 MET cc_start: 0.6926 (ttm) cc_final: 0.6584 (ttp) REVERT: B 42 TRP cc_start: 0.7440 (t60) cc_final: 0.7099 (t60) REVERT: B 153 GLN cc_start: 0.7619 (tt0) cc_final: 0.7269 (tm-30) REVERT: B 260 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7830 (mp0) REVERT: B 405 ARG cc_start: 0.8693 (ppp80) cc_final: 0.8429 (ptm-80) REVERT: B 431 HIS cc_start: 0.8068 (t-90) cc_final: 0.7521 (t-90) REVERT: B 479 TYR cc_start: 0.8607 (t80) cc_final: 0.7904 (t80) outliers start: 33 outliers final: 16 residues processed: 131 average time/residue: 0.3984 time to fit residues: 57.3650 Evaluate side-chains 119 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 623 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 50 optimal weight: 0.0980 chunk 49 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 111 optimal weight: 0.0470 chunk 118 optimal weight: 0.0570 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094301 restraints weight = 15096.585| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.23 r_work: 0.3029 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11049 Z= 0.103 Angle : 0.511 8.615 15079 Z= 0.253 Chirality : 0.036 0.143 1759 Planarity : 0.004 0.072 1769 Dihedral : 9.855 86.521 2342 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.44 % Allowed : 15.43 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.24), residues: 1257 helix: 2.38 (0.17), residues: 942 sheet: None (None), residues: 0 loop : -0.40 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 384 TYR 0.010 0.001 TYR B 662 PHE 0.016 0.001 PHE A 626 TRP 0.024 0.001 TRP B 149 HIS 0.003 0.000 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11046) covalent geometry : angle 0.51145 / 0.25 (15073) SS BOND : bond 0.00060 / 0.03 ( 3) SS BOND : angle 0.24544 / 0.16 ( 6) hydrogen bonds : bond 0.03151 / 2.08 ( 722) hydrogen bonds : angle 3.60874 / 2.71 ( 2142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.335 Fit side-chains REVERT: A 63 ASN cc_start: 0.8484 (m110) cc_final: 0.8033 (m110) REVERT: A 71 MET cc_start: 0.7969 (mpp) cc_final: 0.7552 (mpp) REVERT: A 76 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7255 (mmm160) REVERT: A 80 ASN cc_start: 0.7562 (t0) cc_final: 0.7337 (t0) REVERT: A 139 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7590 (t0) REVERT: A 202 MET cc_start: 0.8083 (mtm) cc_final: 0.7830 (mtp) REVERT: A 339 GLU cc_start: 0.7981 (tt0) cc_final: 0.7483 (mm-30) REVERT: A 494 ARG cc_start: 0.8194 (ttt180) cc_final: 0.7726 (tpp-160) REVERT: A 524 ARG cc_start: 0.7117 (mmt-90) cc_final: 0.6650 (mmp80) REVERT: A 579 MET cc_start: 0.6376 (ttm) cc_final: 0.6092 (ttp) REVERT: B 42 TRP cc_start: 0.7283 (t60) cc_final: 0.6927 (t60) REVERT: B 153 GLN cc_start: 0.7431 (tt0) cc_final: 0.7029 (tm-30) REVERT: B 260 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7549 (mp0) REVERT: B 405 ARG cc_start: 0.8659 (ppp80) cc_final: 0.8388 (ptm-80) REVERT: B 431 HIS cc_start: 0.7851 (t-90) cc_final: 0.7316 (t-90) REVERT: B 479 TYR cc_start: 0.8377 (t80) cc_final: 0.7659 (t80) REVERT: B 516 GLU cc_start: 0.8035 (tp30) cc_final: 0.7686 (tp30) REVERT: B 520 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8472 (mp) outliers start: 27 outliers final: 14 residues processed: 139 average time/residue: 0.3905 time to fit residues: 59.7467 Evaluate side-chains 122 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 623 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092591 restraints weight = 15182.016| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.23 r_work: 0.3004 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11049 Z= 0.125 Angle : 0.526 8.046 15079 Z= 0.260 Chirality : 0.037 0.149 1759 Planarity : 0.004 0.059 1769 Dihedral : 9.791 85.978 2342 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.17 % Allowed : 16.25 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.55 (0.24), residues: 1257 helix: 2.36 (0.17), residues: 941 sheet: None (None), residues: 0 loop : -0.40 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 384 TYR 0.012 0.001 TYR B 432 PHE 0.017 0.001 PHE A 626 TRP 0.027 0.001 TRP B 149 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (11046) covalent geometry : angle 0.52648 / 0.26 (15073) SS BOND : bond 0.00084 / 0.04 ( 3) SS BOND : angle 0.18538 / 0.11 ( 6) hydrogen bonds : bond 0.03277 / 2.17 ( 722) hydrogen bonds : angle 3.63569 / 2.73 ( 2142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.273 Fit side-chains REVERT: A 63 ASN cc_start: 0.8500 (m110) cc_final: 0.8037 (m110) REVERT: A 71 MET cc_start: 0.7989 (mpp) cc_final: 0.7432 (mpp) REVERT: A 76 ARG cc_start: 0.8123 (tpp-160) cc_final: 0.7281 (mmm160) REVERT: A 80 ASN cc_start: 0.7571 (t0) cc_final: 0.7347 (t0) REVERT: A 139 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7610 (t0) REVERT: A 202 MET cc_start: 0.8105 (mtm) cc_final: 0.7877 (mtp) REVERT: A 339 GLU cc_start: 0.8017 (tt0) cc_final: 0.7535 (mm-30) REVERT: A 494 ARG cc_start: 0.8228 (ttt180) cc_final: 0.7747 (tpp-160) REVERT: A 524 ARG cc_start: 0.7081 (mmt-90) cc_final: 0.6629 (mmp80) REVERT: A 579 MET cc_start: 0.6450 (ttm) cc_final: 0.6162 (ttp) REVERT: B 42 TRP cc_start: 0.7390 (t60) cc_final: 0.7043 (t60) REVERT: B 153 GLN cc_start: 0.7455 (tt0) cc_final: 0.7061 (tm-30) REVERT: B 260 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7572 (mp0) REVERT: B 381 GLU cc_start: 0.8754 (pt0) cc_final: 0.8490 (pt0) REVERT: B 405 ARG cc_start: 0.8633 (ppp80) cc_final: 0.8363 (ptm-80) REVERT: B 431 HIS cc_start: 0.7856 (t-90) cc_final: 0.7299 (t-90) REVERT: B 479 TYR cc_start: 0.8406 (t80) cc_final: 0.7726 (t80) outliers start: 24 outliers final: 15 residues processed: 127 average time/residue: 0.3754 time to fit residues: 52.5231 Evaluate side-chains 119 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 623 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 84 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.093739 restraints weight = 15176.197| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.19 r_work: 0.3070 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11049 Z= 0.108 Angle : 0.522 9.485 15079 Z= 0.256 Chirality : 0.037 0.143 1759 Planarity : 0.004 0.053 1769 Dihedral : 9.594 85.300 2342 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.17 % Allowed : 16.43 % Favored : 81.41 % 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: 2.58 (0.24), residues: 1257 helix: 2.39 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 384 TYR 0.009 0.001 TYR B 662 PHE 0.019 0.001 PHE A 427 TRP 0.031 0.001 TRP B 149 HIS 0.003 0.000 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11046) covalent geometry : angle 0.52159 / 0.26 (15073) SS BOND : bond 0.00072 / 0.04 ( 3) SS BOND : angle 0.24316 / 0.15 ( 6) hydrogen bonds : bond 0.03153 / 2.08 ( 722) hydrogen bonds : angle 3.60467 / 2.71 ( 2142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.297 Fit side-chains REVERT: A 63 ASN cc_start: 0.8514 (m110) cc_final: 0.8079 (m110) REVERT: A 71 MET cc_start: 0.8168 (mpp) cc_final: 0.7679 (mpp) REVERT: A 76 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7360 (mmm160) REVERT: A 80 ASN cc_start: 0.7801 (t0) cc_final: 0.7569 (t0) REVERT: A 139 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7843 (t0) REVERT: A 202 MET cc_start: 0.8329 (mtm) cc_final: 0.8028 (mtp) REVERT: A 330 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7831 (ttm-80) REVERT: A 339 GLU cc_start: 0.8137 (tt0) cc_final: 0.7676 (mm-30) REVERT: A 494 ARG cc_start: 0.8253 (ttt180) cc_final: 0.7814 (tpp-160) REVERT: A 524 ARG cc_start: 0.7217 (mmt-90) cc_final: 0.6780 (mmp80) REVERT: A 579 MET cc_start: 0.6769 (ttm) cc_final: 0.6454 (ttp) REVERT: B 153 GLN cc_start: 0.7606 (tt0) cc_final: 0.7167 (tm-30) REVERT: B 260 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7769 (mp0) REVERT: B 381 GLU cc_start: 0.8763 (pt0) cc_final: 0.8485 (pt0) REVERT: B 405 ARG cc_start: 0.8661 (ppp80) cc_final: 0.8438 (ptm-80) REVERT: B 431 HIS cc_start: 0.8053 (t-90) cc_final: 0.7479 (t-90) REVERT: B 479 TYR cc_start: 0.8510 (t80) cc_final: 0.7893 (t80) REVERT: B 516 GLU cc_start: 0.8161 (tp30) cc_final: 0.7922 (tp30) outliers start: 24 outliers final: 15 residues processed: 127 average time/residue: 0.4241 time to fit residues: 58.8162 Evaluate side-chains 118 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 623 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 124 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 0.0020 chunk 61 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.092468 restraints weight = 15196.670| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.24 r_work: 0.3003 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11049 Z= 0.132 Angle : 0.545 9.969 15079 Z= 0.268 Chirality : 0.038 0.147 1759 Planarity : 0.004 0.051 1769 Dihedral : 9.599 84.735 2342 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.81 % Allowed : 16.97 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.24), residues: 1257 helix: 2.37 (0.17), residues: 942 sheet: None (None), residues: 0 loop : -0.38 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 384 TYR 0.011 0.001 TYR B 432 PHE 0.017 0.001 PHE A 626 TRP 0.035 0.001 TRP B 149 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (11046) covalent geometry : angle 0.54525 / 0.27 (15073) SS BOND : bond 0.00084 / 0.04 ( 3) SS BOND : angle 0.18296 / 0.10 ( 6) hydrogen bonds : bond 0.03348 / 2.21 ( 722) hydrogen bonds : angle 3.63513 / 2.73 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.379 Fit side-chains REVERT: A 63 ASN cc_start: 0.8492 (m110) cc_final: 0.8040 (m110) REVERT: A 76 ARG cc_start: 0.8145 (tpp-160) cc_final: 0.7528 (mmm160) REVERT: A 80 ASN cc_start: 0.7576 (t0) cc_final: 0.7355 (t0) REVERT: A 139 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7619 (t0) REVERT: A 202 MET cc_start: 0.8137 (mtm) cc_final: 0.7856 (mtp) REVERT: A 339 GLU cc_start: 0.8036 (tt0) cc_final: 0.7574 (mm-30) REVERT: A 494 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7710 (tpp-160) REVERT: A 524 ARG cc_start: 0.7138 (mmt-90) cc_final: 0.6729 (mmp80) REVERT: A 579 MET cc_start: 0.6418 (ttm) cc_final: 0.6120 (ttp) REVERT: B 153 GLN cc_start: 0.7465 (tt0) cc_final: 0.7043 (tm-30) REVERT: B 260 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7606 (mp0) REVERT: B 405 ARG cc_start: 0.8663 (ppp80) cc_final: 0.8419 (ptm-80) REVERT: B 431 HIS cc_start: 0.7859 (t-90) cc_final: 0.7257 (t-90) REVERT: B 479 TYR cc_start: 0.8402 (t80) cc_final: 0.7811 (t80) outliers start: 20 outliers final: 15 residues processed: 126 average time/residue: 0.4188 time to fit residues: 57.9316 Evaluate side-chains 116 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 623 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 431 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 = 0.3575 r_free = 0.3575 target = 0.123185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092542 restraints weight = 15347.415| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.25 r_work: 0.3010 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11049 Z= 0.126 Angle : 0.548 9.938 15079 Z= 0.270 Chirality : 0.038 0.159 1759 Planarity : 0.004 0.048 1769 Dihedral : 9.563 84.122 2342 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.53 % Allowed : 17.15 % Favored : 81.32 % 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: 2.55 (0.24), residues: 1257 helix: 2.36 (0.17), residues: 941 sheet: None (None), residues: 0 loop : -0.40 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 384 TYR 0.009 0.001 TYR B 662 PHE 0.017 0.001 PHE A 626 TRP 0.038 0.001 TRP B 149 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11046) covalent geometry : angle 0.54813 / 0.27 (15073) SS BOND : bond 0.00082 / 0.04 ( 3) SS BOND : angle 0.18941 / 0.11 ( 6) hydrogen bonds : bond 0.03300 / 2.19 ( 722) hydrogen bonds : angle 3.64979 / 2.74 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2895.66 seconds wall clock time: 50 minutes 0.33 seconds (3000.33 seconds total)