Starting phenix.real_space_refine on Fri Aug 22 18:35:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwt_35779/08_2025/8iwt_35779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwt_35779/08_2025/8iwt_35779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iwt_35779/08_2025/8iwt_35779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwt_35779/08_2025/8iwt_35779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iwt_35779/08_2025/8iwt_35779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwt_35779/08_2025/8iwt_35779.map" } resolution = 3.25 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 52 5.16 5 Be 1 3.05 5 C 4345 2.51 5 N 1137 2.21 5 O 1281 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6820 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6815 Classifications: {'peptide': 891} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 855} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.34, per 1000 atoms: 0.20 Number of scatterers: 6820 At special positions: 0 Unit cell: (91.56, 94.08, 126.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 52 16.00 Mg 1 11.99 F 3 9.00 O 1281 8.00 N 1137 7.00 C 4345 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 271.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 56.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.824A pdb=" N PHE A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.540A pdb=" N LYS A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.632A pdb=" N MET A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 132 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 235 through 238 removed outlier: 3.681A pdb=" N ASN A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 238' Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.891A pdb=" N VAL A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 288 Processing helix chain 'A' and resid 290 through 305 removed outlier: 3.594A pdb=" N MET A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.321A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.311A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.690A pdb=" N LYS A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 602 removed outlier: 3.740A pdb=" N MET A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.673A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 682 through 723 removed outlier: 3.703A pdb=" N MET A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 772 through 800 Processing helix chain 'A' and resid 805 through 826 Processing helix chain 'A' and resid 832 through 836 removed outlier: 3.504A pdb=" N GLU A 835 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 836 " --> pdb=" O VAL A 833 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 832 through 836' Processing helix chain 'A' and resid 841 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 886 through 905 removed outlier: 3.573A pdb=" N LYS A 904 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.863A pdb=" N CYS A 141 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 222 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.863A pdb=" N CYS A 141 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 222 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 595 removed outlier: 8.691A pdb=" N PHE A 617 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET A 568 " --> pdb=" O PHE A 617 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.694A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 476 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.694A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 13.785A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 417 443 hydrogen bonds defined for protein. 1299 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: 0.92 Time building geometry restraints manager: 0.80 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: 1152 1.32 - 1.44: 1618 1.44 - 1.56: 4070 1.56 - 1.69: 3 1.69 - 1.81: 84 Bond restraints: 6927 Sorted by residual: bond pdb=" CA LYS A 351 " pdb=" C LYS A 351 " ideal model delta sigma weight residual 1.525 1.467 0.059 1.02e-02 9.61e+03 3.30e+01 bond pdb=" F2 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CA SER A 901 " pdb=" C SER A 901 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.24e-02 6.50e+03 1.71e+01 bond pdb=" F3 BEF A1001 " pdb="BE BEF A1001 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CA THR A 352 " pdb=" C THR A 352 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.34e-02 5.57e+03 1.03e+01 ... (remaining 6922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 9296 2.75 - 5.50: 72 5.50 - 8.25: 9 8.25 - 11.00: 1 11.00 - 13.75: 2 Bond angle restraints: 9380 Sorted by residual: angle pdb=" N ASP A 350 " pdb=" CA ASP A 350 " pdb=" C ASP A 350 " ideal model delta sigma weight residual 110.53 97.72 12.81 1.29e+00 6.01e-01 9.86e+01 angle pdb=" N SER A 901 " pdb=" CA SER A 901 " pdb=" C SER A 901 " ideal model delta sigma weight residual 110.97 104.48 6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" F2 BEF A1001 " pdb="BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 119.96 106.21 13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N ILE A 233 " pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 113.53 109.48 4.05 9.80e-01 1.04e+00 1.71e+01 angle pdb=" N PRO A 805 " pdb=" CA PRO A 805 " pdb=" C PRO A 805 " ideal model delta sigma weight residual 112.47 120.59 -8.12 2.06e+00 2.36e-01 1.55e+01 ... (remaining 9375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3622 16.92 - 33.84: 450 33.84 - 50.76: 130 50.76 - 67.68: 21 67.68 - 84.60: 9 Dihedral angle restraints: 4232 sinusoidal: 1666 harmonic: 2566 Sorted by residual: dihedral pdb=" CA ASP A 757 " pdb=" CB ASP A 757 " pdb=" CG ASP A 757 " pdb=" OD1 ASP A 757 " ideal model delta sinusoidal sigma weight residual -30.00 -88.42 58.42 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG A 403 " pdb=" CD ARG A 403 " pdb=" NE ARG A 403 " pdb=" CZ ARG A 403 " ideal model delta sinusoidal sigma weight residual -180.00 -137.43 -42.57 2 1.50e+01 4.44e-03 9.76e+00 dihedral pdb=" CA LYS A 327 " pdb=" CB LYS A 327 " pdb=" CG LYS A 327 " pdb=" CD LYS A 327 " ideal model delta sinusoidal sigma weight residual 180.00 120.42 59.58 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 945 0.054 - 0.108: 165 0.108 - 0.162: 14 0.162 - 0.217: 3 0.217 - 0.271: 2 Chirality restraints: 1129 Sorted by residual: chirality pdb=" CA PRO A 805 " pdb=" N PRO A 805 " pdb=" C PRO A 805 " pdb=" CB PRO A 805 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB ILE A 784 " pdb=" CA ILE A 784 " pdb=" CG1 ILE A 784 " pdb=" CG2 ILE A 784 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE A 18 " pdb=" CA ILE A 18 " pdb=" CG1 ILE A 18 " pdb=" CG2 ILE A 18 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1126 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 804 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO A 805 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 253 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 254 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 452 " -0.039 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO A 453 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.032 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 13 2.33 - 2.97: 3241 2.97 - 3.61: 10229 3.61 - 4.26: 14798 4.26 - 4.90: 25505 Nonbonded interactions: 53786 Sorted by model distance: nonbonded pdb=" OD2 ASP A 350 " pdb=" F1 BEF A1001 " model vdw 1.687 2.990 nonbonded pdb=" F1 BEF A1001 " pdb="MG MG A1002 " model vdw 1.757 2.120 nonbonded pdb=" OD2 ASP A 350 " pdb="BE BEF A1001 " model vdw 1.815 1.936 nonbonded pdb=" OD1 ASP A 644 " pdb="MG MG A1002 " model vdw 2.071 2.170 nonbonded pdb=" OD2 ASP A 350 " pdb="MG MG A1002 " model vdw 2.104 2.170 ... (remaining 53781 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.920 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 : 0.010 0.789 6928 Z= 0.973 Angle : 0.633 13.749 9380 Z= 0.371 Chirality : 0.041 0.271 1129 Planarity : 0.006 0.119 1185 Dihedral : 16.196 84.605 2572 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.70 % Favored : 96.96 % Rotamer: Outliers : 0.52 % Allowed : 23.27 % Favored : 76.21 % 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 aren not related in a simple way. whole: 2.49 (0.30), residues: 889 helix: 2.56 (0.23), residues: 510 sheet: 0.43 (0.53), residues: 101 loop : 0.46 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 760 TYR 0.007 0.001 TYR A 510 PHE 0.019 0.001 PHE A 57 TRP 0.002 0.000 TRP A 460 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6927) covalent geometry : angle 0.63273 ( 9380) hydrogen bonds : bond 0.14529 ( 419) hydrogen bonds : angle 5.63873 ( 1299) Misc. bond : bond 0.78865 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.231 Fit side-chains REVERT: A 57 PHE cc_start: 0.7653 (t80) cc_final: 0.7334 (t80) outliers start: 4 outliers final: 1 residues processed: 110 average time/residue: 0.0749 time to fit residues: 11.0023 Evaluate side-chains 102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 901 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.0370 chunk 74 optimal weight: 0.3980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.183113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.158879 restraints weight = 7888.583| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.81 r_work: 0.3639 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 6928 Z= 0.109 Angle : 0.500 9.404 9380 Z= 0.264 Chirality : 0.041 0.305 1129 Planarity : 0.006 0.125 1185 Dihedral : 3.522 19.034 940 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.08 % Rotamer: Outliers : 1.83 % Allowed : 21.57 % Favored : 76.60 % 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 aren not related in a simple way. whole: 2.54 (0.29), residues: 889 helix: 2.78 (0.23), residues: 493 sheet: 0.30 (0.53), residues: 96 loop : 0.35 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 760 TYR 0.007 0.001 TYR A 272 PHE 0.008 0.001 PHE A 538 TRP 0.024 0.001 TRP A 60 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6927) covalent geometry : angle 0.49993 ( 9380) hydrogen bonds : bond 0.03367 ( 419) hydrogen bonds : angle 4.15896 ( 1299) Misc. bond : bond 0.00170 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.259 Fit side-chains REVERT: A 146 LYS cc_start: 0.8284 (pptt) cc_final: 0.8079 (pptt) REVERT: A 154 ASP cc_start: 0.7868 (m-30) cc_final: 0.7624 (t70) REVERT: A 281 MET cc_start: 0.7118 (mmt) cc_final: 0.6233 (mmt) REVERT: A 337 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6689 (mm) REVERT: A 402 SER cc_start: 0.8738 (m) cc_final: 0.8336 (p) REVERT: A 803 ILE cc_start: 0.3606 (OUTLIER) cc_final: 0.3191 (pt) outliers start: 14 outliers final: 6 residues processed: 121 average time/residue: 0.0811 time to fit residues: 13.0517 Evaluate side-chains 110 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 82 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.175884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153882 restraints weight = 7676.797| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.49 r_work: 0.3494 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 6928 Z= 0.144 Angle : 0.535 9.931 9380 Z= 0.284 Chirality : 0.042 0.292 1129 Planarity : 0.006 0.131 1185 Dihedral : 3.728 18.867 939 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.08 % Rotamer: Outliers : 2.88 % Allowed : 21.05 % Favored : 76.08 % 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 aren not related in a simple way. whole: 2.42 (0.29), residues: 889 helix: 2.69 (0.23), residues: 488 sheet: 0.17 (0.47), residues: 114 loop : 0.38 (0.41), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 760 TYR 0.010 0.001 TYR A 272 PHE 0.013 0.001 PHE A 812 TRP 0.009 0.002 TRP A 285 HIS 0.003 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6927) covalent geometry : angle 0.53501 ( 9380) hydrogen bonds : bond 0.04392 ( 419) hydrogen bonds : angle 4.04583 ( 1299) Misc. bond : bond 0.00156 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.164 Fit side-chains REVERT: A 402 SER cc_start: 0.8974 (m) cc_final: 0.8598 (p) outliers start: 22 outliers final: 10 residues processed: 128 average time/residue: 0.0780 time to fit residues: 13.2727 Evaluate side-chains 109 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 82 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.158292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133067 restraints weight = 8131.052| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.89 r_work: 0.3417 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 6928 Z= 0.134 Angle : 0.532 10.455 9380 Z= 0.278 Chirality : 0.041 0.286 1129 Planarity : 0.006 0.134 1185 Dihedral : 3.729 18.226 939 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.25 % Favored : 97.53 % Rotamer: Outliers : 3.14 % Allowed : 22.35 % Favored : 74.51 % 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 aren not related in a simple way. whole: 2.31 (0.29), residues: 889 helix: 2.64 (0.23), residues: 487 sheet: 0.10 (0.44), residues: 123 loop : 0.25 (0.41), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 760 TYR 0.009 0.001 TYR A 272 PHE 0.018 0.001 PHE A 57 TRP 0.008 0.001 TRP A 285 HIS 0.004 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6927) covalent geometry : angle 0.53152 ( 9380) hydrogen bonds : bond 0.04098 ( 419) hydrogen bonds : angle 4.02961 ( 1299) Misc. bond : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.275 Fit side-chains REVERT: A 93 ILE cc_start: 0.8081 (pt) cc_final: 0.7787 (mt) REVERT: A 281 MET cc_start: 0.7116 (mmt) cc_final: 0.6424 (mmt) REVERT: A 337 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7222 (mm) REVERT: A 402 SER cc_start: 0.9034 (m) cc_final: 0.8671 (p) outliers start: 24 outliers final: 13 residues processed: 128 average time/residue: 0.0693 time to fit residues: 12.1393 Evaluate side-chains 118 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 48 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140137 restraints weight = 7881.525| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.48 r_work: 0.3295 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 6928 Z= 0.238 Angle : 0.664 10.559 9380 Z= 0.350 Chirality : 0.045 0.276 1129 Planarity : 0.006 0.136 1185 Dihedral : 4.382 20.543 939 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.04 % Favored : 96.63 % Rotamer: Outliers : 4.31 % Allowed : 21.83 % Favored : 73.86 % 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 aren not related in a simple way. whole: 1.44 (0.28), residues: 889 helix: 1.91 (0.23), residues: 491 sheet: -0.24 (0.41), residues: 124 loop : -0.11 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 54 TYR 0.014 0.001 TYR A 272 PHE 0.025 0.002 PHE A 63 TRP 0.019 0.002 TRP A 285 HIS 0.006 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 6927) covalent geometry : angle 0.66354 ( 9380) hydrogen bonds : bond 0.06151 ( 419) hydrogen bonds : angle 4.53498 ( 1299) Misc. bond : bond 0.00235 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.198 Fit side-chains REVERT: A 28 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6958 (mm-30) REVERT: A 241 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7957 (t80) REVERT: A 281 MET cc_start: 0.7718 (mmt) cc_final: 0.7243 (mmt) REVERT: A 402 SER cc_start: 0.9045 (m) cc_final: 0.8683 (p) REVERT: A 686 MET cc_start: 0.7820 (mtm) cc_final: 0.7523 (mpp) outliers start: 33 outliers final: 19 residues processed: 136 average time/residue: 0.0738 time to fit residues: 13.6587 Evaluate side-chains 120 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.151499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127705 restraints weight = 8128.189| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.68 r_work: 0.3323 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 6928 Z= 0.152 Angle : 0.593 10.793 9380 Z= 0.309 Chirality : 0.042 0.273 1129 Planarity : 0.006 0.137 1185 Dihedral : 4.056 19.333 939 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.59 % Favored : 97.08 % Rotamer: Outliers : 3.01 % Allowed : 23.79 % Favored : 73.20 % 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 aren not related in a simple way. whole: 1.73 (0.29), residues: 889 helix: 2.15 (0.23), residues: 491 sheet: -0.07 (0.43), residues: 117 loop : -0.03 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 760 TYR 0.012 0.001 TYR A 272 PHE 0.013 0.001 PHE A 79 TRP 0.009 0.001 TRP A 285 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6927) covalent geometry : angle 0.59250 ( 9380) hydrogen bonds : bond 0.04780 ( 419) hydrogen bonds : angle 4.25937 ( 1299) Misc. bond : bond 0.00104 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.236 Fit side-chains REVERT: A 28 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6874 (mm-30) REVERT: A 148 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 281 MET cc_start: 0.7353 (mmt) cc_final: 0.6683 (mmt) REVERT: A 327 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7158 (mtpt) REVERT: A 402 SER cc_start: 0.9066 (m) cc_final: 0.8707 (p) REVERT: A 427 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7851 (mt-10) REVERT: A 535 GLN cc_start: 0.8449 (mp10) cc_final: 0.7929 (mp10) REVERT: A 686 MET cc_start: 0.7559 (mtm) cc_final: 0.7118 (mmm) REVERT: A 806 ARG cc_start: 0.5776 (ttt180) cc_final: 0.5176 (ptm160) outliers start: 23 outliers final: 17 residues processed: 132 average time/residue: 0.0740 time to fit residues: 13.2361 Evaluate side-chains 121 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.123874 restraints weight = 8214.300| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.85 r_work: 0.3427 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 6928 Z= 0.164 Angle : 0.599 12.798 9380 Z= 0.311 Chirality : 0.042 0.272 1129 Planarity : 0.006 0.137 1185 Dihedral : 4.047 19.575 939 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.04 % Favored : 96.63 % Rotamer: Outliers : 3.92 % Allowed : 23.01 % Favored : 73.07 % 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 aren not related in a simple way. whole: 1.73 (0.28), residues: 889 helix: 2.18 (0.23), residues: 491 sheet: -0.07 (0.43), residues: 117 loop : -0.10 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 760 TYR 0.011 0.001 TYR A 272 PHE 0.014 0.001 PHE A 812 TRP 0.011 0.001 TRP A 285 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6927) covalent geometry : angle 0.59906 ( 9380) hydrogen bonds : bond 0.04891 ( 419) hydrogen bonds : angle 4.24001 ( 1299) Misc. bond : bond 0.00146 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.192 Fit side-chains REVERT: A 28 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7040 (mm-30) REVERT: A 53 HIS cc_start: 0.6368 (OUTLIER) cc_final: 0.4911 (t-90) REVERT: A 149 HIS cc_start: 0.7446 (m-70) cc_final: 0.7037 (m90) REVERT: A 281 MET cc_start: 0.7585 (mmt) cc_final: 0.7165 (mmt) REVERT: A 327 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7301 (mtpt) REVERT: A 402 SER cc_start: 0.9141 (m) cc_final: 0.8820 (p) REVERT: A 427 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 535 GLN cc_start: 0.8492 (mp10) cc_final: 0.7979 (mp10) REVERT: A 641 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7881 (ttt) REVERT: A 686 MET cc_start: 0.7757 (mtm) cc_final: 0.7446 (mmm) REVERT: A 806 ARG cc_start: 0.5939 (ttt180) cc_final: 0.5383 (ptm160) outliers start: 30 outliers final: 25 residues processed: 130 average time/residue: 0.0744 time to fit residues: 13.3371 Evaluate side-chains 134 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.149210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124292 restraints weight = 8300.369| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.86 r_work: 0.3432 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 6928 Z= 0.153 Angle : 0.596 10.726 9380 Z= 0.310 Chirality : 0.042 0.271 1129 Planarity : 0.006 0.137 1185 Dihedral : 4.022 19.373 939 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.15 % Favored : 96.51 % Rotamer: Outliers : 3.92 % Allowed : 23.79 % Favored : 72.29 % 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 aren not related in a simple way. whole: 1.76 (0.29), residues: 889 helix: 2.19 (0.23), residues: 493 sheet: -0.02 (0.43), residues: 117 loop : -0.08 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 760 TYR 0.011 0.001 TYR A 272 PHE 0.013 0.001 PHE A 812 TRP 0.009 0.001 TRP A 285 HIS 0.007 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6927) covalent geometry : angle 0.59574 ( 9380) hydrogen bonds : bond 0.04686 ( 419) hydrogen bonds : angle 4.21778 ( 1299) Misc. bond : bond 0.00109 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.287 Fit side-chains REVERT: A 28 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 281 MET cc_start: 0.7430 (mmt) cc_final: 0.6902 (mmt) REVERT: A 402 SER cc_start: 0.9129 (m) cc_final: 0.8806 (p) REVERT: A 427 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7976 (mt-10) REVERT: A 686 MET cc_start: 0.7696 (mtm) cc_final: 0.7401 (mmm) REVERT: A 806 ARG cc_start: 0.5927 (ttt180) cc_final: 0.5369 (ptm160) outliers start: 30 outliers final: 24 residues processed: 129 average time/residue: 0.0700 time to fit residues: 12.4903 Evaluate side-chains 125 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 796 ARG Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.168059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146679 restraints weight = 7783.879| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.45 r_work: 0.3386 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 6928 Z= 0.130 Angle : 0.587 13.240 9380 Z= 0.301 Chirality : 0.042 0.271 1129 Planarity : 0.006 0.136 1185 Dihedral : 3.909 19.116 939 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.92 % Favored : 96.74 % Rotamer: Outliers : 3.27 % Allowed : 24.71 % Favored : 72.03 % 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 aren not related in a simple way. whole: 1.99 (0.29), residues: 889 helix: 2.50 (0.23), residues: 485 sheet: -0.11 (0.43), residues: 124 loop : -0.08 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 760 TYR 0.011 0.001 TYR A 510 PHE 0.012 0.001 PHE A 812 TRP 0.007 0.001 TRP A 285 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6927) covalent geometry : angle 0.58683 ( 9380) hydrogen bonds : bond 0.04158 ( 419) hydrogen bonds : angle 4.11849 ( 1299) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.208 Fit side-chains REVERT: A 53 HIS cc_start: 0.6267 (OUTLIER) cc_final: 0.5469 (t-90) REVERT: A 241 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7907 (t80) REVERT: A 281 MET cc_start: 0.7281 (mmt) cc_final: 0.6909 (mmt) REVERT: A 402 SER cc_start: 0.9058 (m) cc_final: 0.8707 (p) REVERT: A 427 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 686 MET cc_start: 0.7302 (mtm) cc_final: 0.6992 (mmm) REVERT: A 806 ARG cc_start: 0.5802 (ttt180) cc_final: 0.5228 (ptm160) outliers start: 25 outliers final: 22 residues processed: 123 average time/residue: 0.0745 time to fit residues: 12.5179 Evaluate side-chains 123 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 796 ARG Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 61 ASN ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.165879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142786 restraints weight = 7829.632| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.62 r_work: 0.3355 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 6928 Z= 0.130 Angle : 0.593 12.396 9380 Z= 0.304 Chirality : 0.042 0.270 1129 Planarity : 0.006 0.136 1185 Dihedral : 3.881 19.086 939 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.04 % Favored : 96.63 % Rotamer: Outliers : 3.40 % Allowed : 24.71 % Favored : 71.90 % 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 aren not related in a simple way. whole: 2.03 (0.29), residues: 889 helix: 2.51 (0.23), residues: 487 sheet: -0.09 (0.44), residues: 124 loop : -0.03 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 900 TYR 0.010 0.001 TYR A 510 PHE 0.012 0.001 PHE A 812 TRP 0.007 0.001 TRP A 285 HIS 0.013 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6927) covalent geometry : angle 0.59293 ( 9380) hydrogen bonds : bond 0.04127 ( 419) hydrogen bonds : angle 4.09386 ( 1299) Misc. bond : bond 0.00055 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.221 Fit side-chains REVERT: A 53 HIS cc_start: 0.6177 (OUTLIER) cc_final: 0.4476 (t-90) REVERT: A 241 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7974 (t80) REVERT: A 281 MET cc_start: 0.7254 (mmt) cc_final: 0.6941 (mmt) REVERT: A 402 SER cc_start: 0.9064 (m) cc_final: 0.8700 (p) REVERT: A 427 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7791 (mt-10) REVERT: A 686 MET cc_start: 0.7338 (mtm) cc_final: 0.7006 (mmm) REVERT: A 806 ARG cc_start: 0.5759 (ttt180) cc_final: 0.5178 (ptm160) outliers start: 26 outliers final: 22 residues processed: 118 average time/residue: 0.0678 time to fit residues: 11.0082 Evaluate side-chains 123 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 796 ARG Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 0.0040 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 61 ASN ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127425 restraints weight = 8226.037| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.82 r_work: 0.3365 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 6928 Z= 0.138 Angle : 0.597 12.277 9380 Z= 0.305 Chirality : 0.042 0.270 1129 Planarity : 0.006 0.136 1185 Dihedral : 3.901 19.198 939 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.26 % Favored : 96.40 % Rotamer: Outliers : 3.27 % Allowed : 24.58 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.29), residues: 889 helix: 2.50 (0.23), residues: 487 sheet: -0.08 (0.44), residues: 124 loop : -0.03 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 900 TYR 0.009 0.001 TYR A 510 PHE 0.012 0.001 PHE A 812 TRP 0.008 0.001 TRP A 285 HIS 0.012 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6927) covalent geometry : angle 0.59657 ( 9380) hydrogen bonds : bond 0.04217 ( 419) hydrogen bonds : angle 4.10361 ( 1299) Misc. bond : bond 0.00073 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.43 seconds wall clock time: 32 minutes 28.97 seconds (1948.97 seconds total)