Starting phenix.real_space_refine on Tue Mar 3 16:31:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v4u_21048/03_2026/6v4u_21048.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4u_21048/03_2026/6v4u_21048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v4u_21048/03_2026/6v4u_21048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4u_21048/03_2026/6v4u_21048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v4u_21048/03_2026/6v4u_21048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4u_21048/03_2026/6v4u_21048.map" } resolution = 3.8 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= 0.039 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4443 2.51 5 N 1262 2.21 5 O 1346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2475 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 324} Chain breaks: 7 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2075 Classifications: {'peptide': 356} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 221} Link IDs: {'PTRANS': 14, 'TRANS': 341} Chain breaks: 7 Unresolved non-hydrogen bonds: 785 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 630 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'TRP:plan': 3, 'ASP:plan': 20, 'ASN:plan1': 8, 'ARG:plan': 15, 'HIS:plan': 3, 'GLU:plan': 16, 'PHE:plan': 12, 'GLN:plan1': 9, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 401 Chain: "B" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 2524 Classifications: {'peptide': 421} Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 231} Link IDs: {'PTRANS': 12, 'TRANS': 408} Chain breaks: 11 Unresolved non-hydrogen bonds: 944 Unresolved non-hydrogen angles: 1200 Unresolved non-hydrogen dihedrals: 776 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'ARG:plan': 21, 'ASP:plan': 19, 'PHE:plan': 14, 'GLU:plan': 24, 'ASN:plan1': 6, 'TYR:plan': 10, 'HIS:plan': 8, 'GLN:plan1': 12, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 541 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG C 347 " occ=0.81 ... (9 atoms not shown) pdb=" NH2 ARG C 347 " occ=0.71 Time building chain proxies: 1.81, per 1000 atoms: 0.26 Number of scatterers: 7074 At special positions: 0 Unit cell: (74.698, 122.964, 155.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1346 8.00 N 1262 7.00 C 4443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 282.0 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 40.5% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'C' and resid 444 through 451 Processing helix chain 'A' and resid 55 through 69 removed outlier: 4.008A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.511A pdb=" N LEU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 141 removed outlier: 3.631A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.632A pdb=" N THR A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 removed outlier: 4.180A pdb=" N ILE A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.779A pdb=" N TYR A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.953A pdb=" N LEU A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.702A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 439 removed outlier: 3.862A pdb=" N LYS A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 4.472A pdb=" N MET A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Proline residue: A 457 - end of helix Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'B' and resid 83 through 98 removed outlier: 5.647A pdb=" N TYR B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 217 removed outlier: 3.738A pdb=" N ALA B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 253 Processing helix chain 'B' and resid 321 through 340 removed outlier: 3.543A pdb=" N THR B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 359 Processing helix chain 'B' and resid 366 through 382 Processing helix chain 'B' and resid 707 through 716 Processing helix chain 'B' and resid 719 through 730 removed outlier: 3.955A pdb=" N ALA B 723 " --> pdb=" O PHE B 719 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 746 removed outlier: 3.592A pdb=" N LEU B 746 " --> pdb=" O ILE B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.507A pdb=" N LEU B 750 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 751 " --> pdb=" O THR B 748 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE B 752 " --> pdb=" O ALA B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 747 through 752' Processing helix chain 'B' and resid 771 through 779 removed outlier: 3.936A pdb=" N MET B 775 " --> pdb=" O PRO B 771 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 777 " --> pdb=" O HIS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 832 Processing helix chain 'B' and resid 842 through 868 Processing helix chain 'B' and resid 880 through 892 Processing helix chain 'B' and resid 900 through 914 Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.638A pdb=" N LEU C 37 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 39 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 428 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 429 " --> pdb=" O THR C 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 50 removed outlier: 6.835A pdb=" N ALA C 60 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 49 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA C 58 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'C' and resid 105 through 109 removed outlier: 4.084A pdb=" N VAL C 117 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN C 127 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AA6, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 332 Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 43 removed outlier: 3.631A pdb=" N ARG A 40 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 27 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR A 109 " --> pdb=" O TRP A 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AB1, first strand: chain 'B' and resid 784 through 786 removed outlier: 8.209A pdb=" N LEU B 785 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL B 735 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR B 732 " --> pdb=" O SER B 808 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 810 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 734 " --> pdb=" O LEU B 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 322 hydrogen bonds defined for protein. 945 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: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2456 1.34 - 1.46: 1512 1.46 - 1.58: 3169 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 7167 Sorted by residual: bond pdb=" N GLU A 442 " pdb=" CA GLU A 442 " ideal model delta sigma weight residual 1.456 1.469 -0.013 1.25e-02 6.40e+03 1.12e+00 bond pdb=" CA ASP C 163 " pdb=" CB ASP C 163 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.14e-01 bond pdb=" C LYS B 762 " pdb=" N PRO B 763 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.56e-01 bond pdb=" CA THR C 123 " pdb=" CB THR C 123 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.55e-01 bond pdb=" CA SER A 23 " pdb=" C SER A 23 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.10e-02 2.27e+03 5.11e-01 ... (remaining 7162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 9696 1.64 - 3.28: 89 3.28 - 4.93: 23 4.93 - 6.57: 7 6.57 - 8.21: 2 Bond angle restraints: 9817 Sorted by residual: angle pdb=" N ILE A 224 " pdb=" CA ILE A 224 " pdb=" C ILE A 224 " ideal model delta sigma weight residual 111.91 109.33 2.58 8.90e-01 1.26e+00 8.43e+00 angle pdb=" C GLU A 442 " pdb=" CA GLU A 442 " pdb=" CB GLU A 442 " ideal model delta sigma weight residual 109.62 114.66 -5.04 1.79e+00 3.12e-01 7.92e+00 angle pdb=" C LEU C 162 " pdb=" N ASP C 163 " pdb=" CA ASP C 163 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.90e+00 angle pdb=" C THR C 122 " pdb=" N THR C 123 " pdb=" CA THR C 123 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.97e+00 angle pdb=" C MET C 255 " pdb=" N GLN C 256 " pdb=" CA GLN C 256 " ideal model delta sigma weight residual 121.54 125.61 -4.07 1.91e+00 2.74e-01 4.54e+00 ... (remaining 9812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.74: 3825 11.74 - 23.48: 238 23.48 - 35.22: 79 35.22 - 46.96: 22 46.96 - 58.70: 2 Dihedral angle restraints: 4166 sinusoidal: 999 harmonic: 3167 Sorted by residual: dihedral pdb=" CA GLN B 365 " pdb=" C GLN B 365 " pdb=" N HIS B 366 " pdb=" CA HIS B 366 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE B 85 " pdb=" C PHE B 85 " pdb=" N ASP B 86 " pdb=" CA ASP B 86 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA LEU B 711 " pdb=" CB LEU B 711 " pdb=" CG LEU B 711 " pdb=" CD1 LEU B 711 " ideal model delta sinusoidal sigma weight residual 180.00 135.03 44.97 3 1.50e+01 4.44e-03 8.09e+00 ... (remaining 4163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 712 0.028 - 0.056: 330 0.056 - 0.084: 95 0.084 - 0.112: 79 0.112 - 0.140: 10 Chirality restraints: 1226 Sorted by residual: chirality pdb=" CA ASP C 163 " pdb=" N ASP C 163 " pdb=" C ASP C 163 " pdb=" CB ASP C 163 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA VAL C 231 " pdb=" N VAL C 231 " pdb=" C VAL C 231 " pdb=" CB VAL C 231 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE C 402 " pdb=" N ILE C 402 " pdb=" C ILE C 402 " pdb=" CB ILE C 402 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1223 not shown) Planarity restraints: 1294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 466 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 467 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 332 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO C 333 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 182 " -0.016 5.00e-02 4.00e+02 2.44e-02 9.54e-01 pdb=" N PRO C 183 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.014 5.00e-02 4.00e+02 ... (remaining 1291 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1966 2.80 - 3.32: 6433 3.32 - 3.85: 11052 3.85 - 4.37: 11027 4.37 - 4.90: 19623 Nonbonded interactions: 50101 Sorted by model distance: nonbonded pdb=" O LEU B 750 " pdb=" OH TYR B 760 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP C 233 " pdb=" OG SER C 235 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASN C 232 " pdb=" OG1 THR C 290 " model vdw 2.329 3.040 nonbonded pdb=" N GLU C 409 " pdb=" O CYS C 422 " model vdw 2.345 3.120 nonbonded pdb=" O ALA B 706 " pdb=" OG1 THR B 748 " model vdw 2.356 3.040 ... (remaining 50096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.280 Find NCS groups from input model: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 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 : 0.002 0.021 7167 Z= 0.083 Angle : 0.471 8.209 9817 Z= 0.237 Chirality : 0.041 0.140 1226 Planarity : 0.003 0.029 1294 Dihedral : 9.643 58.703 2096 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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: -3.58 (0.23), residues: 1050 helix: 0.19 (0.23), residues: 411 sheet: -4.40 (0.39), residues: 76 loop : -4.35 (0.19), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 160 TYR 0.004 0.000 TYR B 99 PHE 0.008 0.001 PHE B 372 TRP 0.003 0.000 TRP C 148 HIS 0.002 0.000 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00155 ( 7167) covalent geometry : angle 0.47074 ( 9817) hydrogen bonds : bond 0.13517 ( 322) hydrogen bonds : angle 5.82217 ( 945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 LYS cc_start: 0.6796 (tppt) cc_final: 0.6447 (tppt) REVERT: C 211 ASP cc_start: 0.4780 (m-30) cc_final: 0.3465 (m-30) REVERT: A 385 PHE cc_start: 0.4738 (m-10) cc_final: 0.4290 (m-80) REVERT: A 417 GLU cc_start: 0.5917 (mm-30) cc_final: 0.5697 (mm-30) REVERT: A 479 MET cc_start: 0.8090 (mmt) cc_final: 0.7830 (mpp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0765 time to fit residues: 15.5695 Evaluate side-chains 94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.0270 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 HIS B 337 GLN B 356 GLN B 708 GLN B 848 GLN B 903 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.140692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.123137 restraints weight = 23079.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.126090 restraints weight = 13591.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.128281 restraints weight = 9129.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.129846 restraints weight = 6680.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.130765 restraints weight = 5194.105| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4253 r_free = 0.4253 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4249 r_free = 0.4249 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7167 Z= 0.107 Angle : 0.537 8.230 9817 Z= 0.267 Chirality : 0.043 0.139 1226 Planarity : 0.004 0.065 1294 Dihedral : 2.867 15.460 1110 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.44 % Allowed : 16.70 % Favored : 80.86 % 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 are not related in a simple way. whole: -2.50 (0.25), residues: 1050 helix: 1.53 (0.25), residues: 412 sheet: -4.20 (0.37), residues: 88 loop : -4.04 (0.21), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 407 TYR 0.023 0.002 TYR C 413 PHE 0.023 0.002 PHE B 345 TRP 0.017 0.002 TRP C 148 HIS 0.008 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7167) covalent geometry : angle 0.53742 ( 9817) hydrogen bonds : bond 0.02506 ( 322) hydrogen bonds : angle 4.24491 ( 945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: C 40 LYS cc_start: 0.7100 (tppt) cc_final: 0.6872 (tppt) REVERT: C 252 ASP cc_start: 0.8243 (p0) cc_final: 0.8034 (p0) REVERT: A 417 GLU cc_start: 0.6222 (mm-30) cc_final: 0.5954 (mm-30) REVERT: A 479 MET cc_start: 0.8265 (mmt) cc_final: 0.7954 (mpp) outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 0.0781 time to fit residues: 11.7279 Evaluate side-chains 93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 380 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS B 721 HIS B 868 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.122012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.105916 restraints weight = 24688.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.108463 restraints weight = 15257.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.110223 restraints weight = 10582.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.111481 restraints weight = 8003.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.112295 restraints weight = 6463.221| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3988 r_free = 0.3988 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3988 r_free = 0.3988 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 7167 Z= 0.322 Angle : 0.788 9.065 9817 Z= 0.421 Chirality : 0.049 0.190 1226 Planarity : 0.005 0.076 1294 Dihedral : 5.130 25.446 1110 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 5.70 % Allowed : 20.77 % Favored : 73.52 % 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: -2.86 (0.25), residues: 1050 helix: 0.96 (0.26), residues: 417 sheet: -3.86 (0.38), residues: 129 loop : -4.07 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 335 TYR 0.026 0.003 TYR B 913 PHE 0.028 0.003 PHE B 345 TRP 0.027 0.003 TRP C 431 HIS 0.009 0.002 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00684 ( 7167) covalent geometry : angle 0.78802 ( 9817) hydrogen bonds : bond 0.04846 ( 322) hydrogen bonds : angle 5.22728 ( 945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: C 40 LYS cc_start: 0.7687 (tppt) cc_final: 0.7340 (tppp) REVERT: C 322 HIS cc_start: 0.5079 (OUTLIER) cc_final: 0.4061 (m90) REVERT: A 61 PHE cc_start: 0.9118 (t80) cc_final: 0.8773 (t80) REVERT: A 417 GLU cc_start: 0.6362 (mm-30) cc_final: 0.5971 (mm-30) REVERT: B 927 PHE cc_start: 0.4554 (m-80) cc_final: 0.3651 (m-80) outliers start: 28 outliers final: 18 residues processed: 117 average time/residue: 0.0752 time to fit residues: 12.0707 Evaluate side-chains 102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 901 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS B 848 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.125482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.108740 restraints weight = 24381.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.111595 restraints weight = 14550.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.113448 restraints weight = 9840.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.114882 restraints weight = 7338.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.115777 restraints weight = 5840.381| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7167 Z= 0.133 Angle : 0.607 9.467 9817 Z= 0.311 Chirality : 0.044 0.156 1226 Planarity : 0.004 0.070 1294 Dihedral : 4.165 16.723 1110 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.68 % Allowed : 26.07 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.26), residues: 1050 helix: 1.68 (0.27), residues: 411 sheet: -4.26 (0.37), residues: 105 loop : -3.85 (0.23), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 199 TYR 0.021 0.002 TYR C 413 PHE 0.027 0.002 PHE B 345 TRP 0.013 0.002 TRP C 148 HIS 0.015 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7167) covalent geometry : angle 0.60707 ( 9817) hydrogen bonds : bond 0.03258 ( 322) hydrogen bonds : angle 4.45597 ( 945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: C 302 ARG cc_start: 0.5718 (tpt90) cc_final: 0.5421 (tpt90) REVERT: A 417 GLU cc_start: 0.5869 (mm-30) cc_final: 0.5517 (mm-30) REVERT: A 479 MET cc_start: 0.8101 (mmm) cc_final: 0.7681 (mmt) REVERT: B 135 TYR cc_start: 0.8088 (t80) cc_final: 0.7805 (t80) REVERT: B 850 MET cc_start: 0.7905 (mpp) cc_final: 0.7490 (mpp) REVERT: B 927 PHE cc_start: 0.4506 (m-80) cc_final: 0.4110 (m-80) outliers start: 23 outliers final: 13 residues processed: 109 average time/residue: 0.0704 time to fit residues: 10.9005 Evaluate side-chains 98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 368 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.118066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.102036 restraints weight = 25072.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.104622 restraints weight = 15290.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.106430 restraints weight = 10464.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.107724 restraints weight = 7785.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.108563 restraints weight = 6212.902| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7167 Z= 0.241 Angle : 0.744 10.280 9817 Z= 0.391 Chirality : 0.048 0.178 1226 Planarity : 0.005 0.079 1294 Dihedral : 5.127 25.680 1110 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % Rotamer: Outliers : 7.13 % Allowed : 22.81 % Favored : 70.06 % 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: -2.59 (0.26), residues: 1050 helix: 1.07 (0.27), residues: 418 sheet: -3.69 (0.43), residues: 114 loop : -3.84 (0.23), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 331 TYR 0.022 0.002 TYR C 413 PHE 0.027 0.003 PHE B 345 TRP 0.028 0.003 TRP C 148 HIS 0.029 0.002 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 7167) covalent geometry : angle 0.74421 ( 9817) hydrogen bonds : bond 0.04424 ( 322) hydrogen bonds : angle 5.01629 ( 945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: C 37 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5242 (tt) REVERT: C 332 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8686 (mp) REVERT: A 61 PHE cc_start: 0.9045 (t80) cc_final: 0.8721 (t80) REVERT: A 417 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6445 (mm-30) REVERT: A 479 MET cc_start: 0.8098 (mmm) cc_final: 0.7372 (mpp) REVERT: B 850 MET cc_start: 0.7840 (tpp) cc_final: 0.7337 (mpp) REVERT: B 927 PHE cc_start: 0.4902 (m-80) cc_final: 0.4464 (m-80) outliers start: 35 outliers final: 21 residues processed: 110 average time/residue: 0.0751 time to fit residues: 11.5261 Evaluate side-chains 95 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 901 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 94 optimal weight: 0.0000 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 33 optimal weight: 0.0270 chunk 79 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.7046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 HIS B 848 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.123323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.106592 restraints weight = 24564.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.109373 restraints weight = 14876.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.111337 restraints weight = 10129.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.112731 restraints weight = 7523.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.113696 restraints weight = 5956.341| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7167 Z= 0.120 Angle : 0.630 9.493 9817 Z= 0.318 Chirality : 0.045 0.166 1226 Planarity : 0.004 0.074 1294 Dihedral : 4.294 19.125 1110 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 5.09 % Allowed : 26.27 % Favored : 68.64 % 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: -2.25 (0.26), residues: 1050 helix: 1.62 (0.27), residues: 417 sheet: -3.97 (0.39), residues: 107 loop : -3.80 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 331 TYR 0.022 0.002 TYR C 413 PHE 0.028 0.002 PHE B 345 TRP 0.024 0.002 TRP C 148 HIS 0.008 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7167) covalent geometry : angle 0.62976 ( 9817) hydrogen bonds : bond 0.03238 ( 322) hydrogen bonds : angle 4.34731 ( 945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: C 302 ARG cc_start: 0.5400 (tpt90) cc_final: 0.4973 (tpt90) REVERT: A 61 PHE cc_start: 0.9110 (t80) cc_final: 0.8760 (t80) REVERT: A 97 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 417 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6163 (mm-30) REVERT: A 479 MET cc_start: 0.8130 (mmm) cc_final: 0.7432 (mpp) REVERT: B 850 MET cc_start: 0.7931 (tpp) cc_final: 0.7403 (mpp) REVERT: B 927 PHE cc_start: 0.5041 (m-80) cc_final: 0.4588 (m-80) outliers start: 25 outliers final: 18 residues processed: 104 average time/residue: 0.0711 time to fit residues: 10.4902 Evaluate side-chains 96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN A 128 HIS B 848 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.123216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.106520 restraints weight = 24358.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.109201 restraints weight = 14774.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.111147 restraints weight = 10149.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.112575 restraints weight = 7569.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.113564 restraints weight = 5985.096| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7167 Z= 0.122 Angle : 0.631 9.473 9817 Z= 0.313 Chirality : 0.045 0.158 1226 Planarity : 0.004 0.077 1294 Dihedral : 4.149 18.762 1110 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 4.89 % Allowed : 27.09 % Favored : 68.02 % 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: -2.12 (0.27), residues: 1050 helix: 1.68 (0.27), residues: 417 sheet: -3.86 (0.40), residues: 107 loop : -3.70 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 199 TYR 0.017 0.002 TYR C 413 PHE 0.028 0.002 PHE B 345 TRP 0.025 0.002 TRP C 148 HIS 0.006 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7167) covalent geometry : angle 0.63090 ( 9817) hydrogen bonds : bond 0.03195 ( 322) hydrogen bonds : angle 4.30615 ( 945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8588 (mp) REVERT: A 417 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6187 (mm-30) REVERT: A 479 MET cc_start: 0.8091 (mmm) cc_final: 0.7435 (mpp) REVERT: B 850 MET cc_start: 0.7807 (tpp) cc_final: 0.7318 (mpp) REVERT: B 927 PHE cc_start: 0.5032 (m-80) cc_final: 0.4546 (m-80) outliers start: 24 outliers final: 22 residues processed: 101 average time/residue: 0.0677 time to fit residues: 9.7817 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 20 optimal weight: 0.2980 chunk 49 optimal weight: 10.0000 chunk 59 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 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 = 0.4191 r_free = 0.4191 target = 0.123390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.106612 restraints weight = 24039.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.109364 restraints weight = 14680.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.110957 restraints weight = 10048.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.112508 restraints weight = 7827.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.113467 restraints weight = 6144.289| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7167 Z= 0.121 Angle : 0.645 12.221 9817 Z= 0.314 Chirality : 0.045 0.163 1226 Planarity : 0.004 0.079 1294 Dihedral : 4.077 18.311 1110 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 5.09 % Allowed : 27.29 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.27), residues: 1050 helix: 1.77 (0.27), residues: 417 sheet: -3.74 (0.41), residues: 107 loop : -3.58 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 335 TYR 0.021 0.002 TYR B 904 PHE 0.010 0.001 PHE C 297 TRP 0.027 0.002 TRP C 148 HIS 0.005 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7167) covalent geometry : angle 0.64500 ( 9817) hydrogen bonds : bond 0.03179 ( 322) hydrogen bonds : angle 4.23365 ( 945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: C 40 LYS cc_start: 0.7211 (tppt) cc_final: 0.7008 (mmtm) REVERT: C 119 ASP cc_start: 0.7880 (t0) cc_final: 0.7585 (t0) REVERT: C 302 ARG cc_start: 0.5657 (tpt90) cc_final: 0.5388 (tpt90) REVERT: A 97 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8564 (mp) REVERT: A 124 TYR cc_start: 0.8275 (t80) cc_final: 0.7973 (t80) REVERT: A 417 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6195 (mm-30) REVERT: A 479 MET cc_start: 0.8225 (mmm) cc_final: 0.7575 (mpp) REVERT: B 850 MET cc_start: 0.7778 (tpp) cc_final: 0.7257 (mpp) REVERT: B 927 PHE cc_start: 0.5054 (OUTLIER) cc_final: 0.4556 (m-80) outliers start: 25 outliers final: 22 residues processed: 102 average time/residue: 0.0651 time to fit residues: 9.5190 Evaluate side-chains 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 927 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 HIS ** C 256 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 = 0.4208 r_free = 0.4208 target = 0.124798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.108328 restraints weight = 23958.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.110973 restraints weight = 14450.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.112888 restraints weight = 9942.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.114028 restraints weight = 7437.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.115212 restraints weight = 6000.043| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7167 Z= 0.111 Angle : 0.632 11.760 9817 Z= 0.306 Chirality : 0.044 0.156 1226 Planarity : 0.004 0.078 1294 Dihedral : 3.917 18.644 1110 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 5.50 % Allowed : 27.29 % Favored : 67.21 % 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 are not related in a simple way. whole: -1.85 (0.27), residues: 1050 helix: 1.84 (0.27), residues: 421 sheet: -3.80 (0.42), residues: 105 loop : -3.50 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 335 TYR 0.039 0.002 TYR B 904 PHE 0.012 0.001 PHE C 132 TRP 0.027 0.002 TRP C 148 HIS 0.005 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7167) covalent geometry : angle 0.63192 ( 9817) hydrogen bonds : bond 0.02978 ( 322) hydrogen bonds : angle 4.11464 ( 945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: C 302 ARG cc_start: 0.5430 (tpt90) cc_final: 0.4900 (tpt90) REVERT: A 97 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 124 TYR cc_start: 0.8250 (t80) cc_final: 0.7952 (t80) REVERT: A 417 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6185 (mm-30) REVERT: A 479 MET cc_start: 0.8204 (mmm) cc_final: 0.7560 (mpp) REVERT: B 850 MET cc_start: 0.7795 (tpp) cc_final: 0.7296 (mpp) REVERT: B 903 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: B 927 PHE cc_start: 0.4960 (OUTLIER) cc_final: 0.4462 (m-80) outliers start: 27 outliers final: 21 residues processed: 104 average time/residue: 0.0657 time to fit residues: 9.7421 Evaluate side-chains 104 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 927 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 39 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.115427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.099579 restraints weight = 25321.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.102132 restraints weight = 15240.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.103821 restraints weight = 10399.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.105021 restraints weight = 7814.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.106034 restraints weight = 6285.784| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3902 r_free = 0.3902 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3902 r_free = 0.3902 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7167 Z= 0.248 Angle : 0.807 10.573 9817 Z= 0.414 Chirality : 0.049 0.202 1226 Planarity : 0.005 0.091 1294 Dihedral : 5.345 27.124 1110 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.90 % Favored : 84.10 % Rotamer: Outliers : 5.70 % Allowed : 27.49 % Favored : 66.80 % 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: -2.43 (0.26), residues: 1050 helix: 1.11 (0.27), residues: 425 sheet: -3.51 (0.40), residues: 125 loop : -3.74 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 331 TYR 0.034 0.003 TYR B 904 PHE 0.018 0.002 PHE A 84 TRP 0.026 0.003 TRP C 431 HIS 0.011 0.002 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 7167) covalent geometry : angle 0.80695 ( 9817) hydrogen bonds : bond 0.04603 ( 322) hydrogen bonds : angle 5.11140 ( 945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.207 Fit side-chains REVERT: A 61 PHE cc_start: 0.9151 (t80) cc_final: 0.8809 (t80) REVERT: A 97 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8512 (mp) REVERT: A 417 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6386 (mm-30) REVERT: A 479 MET cc_start: 0.8254 (mmm) cc_final: 0.7259 (mpp) REVERT: B 850 MET cc_start: 0.7860 (tpp) cc_final: 0.7405 (mpp) REVERT: B 903 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: B 927 PHE cc_start: 0.5243 (OUTLIER) cc_final: 0.4822 (m-80) outliers start: 28 outliers final: 23 residues processed: 106 average time/residue: 0.0680 time to fit residues: 10.2734 Evaluate side-chains 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 927 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 79 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.121264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.105252 restraints weight = 24298.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.107995 restraints weight = 14255.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.109800 restraints weight = 9615.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.111208 restraints weight = 7156.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.112036 restraints weight = 5664.830| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7167 Z= 0.127 Angle : 0.693 11.573 9817 Z= 0.344 Chirality : 0.045 0.169 1226 Planarity : 0.005 0.097 1294 Dihedral : 4.479 19.759 1110 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 5.50 % Allowed : 28.31 % Favored : 66.19 % 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 (0.27), residues: 1050 helix: 1.63 (0.27), residues: 416 sheet: -3.46 (0.43), residues: 113 loop : -3.65 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 199 TYR 0.038 0.002 TYR B 904 PHE 0.013 0.001 PHE B 372 TRP 0.048 0.003 TRP C 210 HIS 0.008 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7167) covalent geometry : angle 0.69299 ( 9817) hydrogen bonds : bond 0.03567 ( 322) hydrogen bonds : angle 4.48346 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1634.36 seconds wall clock time: 28 minutes 32.71 seconds (1712.71 seconds total)