Starting phenix.real_space_refine on Sat Aug 23 00:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jio_36322/08_2025/8jio_36322.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jio_36322/08_2025/8jio_36322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jio_36322/08_2025/8jio_36322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jio_36322/08_2025/8jio_36322.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jio_36322/08_2025/8jio_36322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jio_36322/08_2025/8jio_36322.map" } resolution = 3.3 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= 0.031 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 34 5.16 5 C 5524 2.51 5 N 1452 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8698 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5350 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 35, 'TRANS': 641} Chain: "B" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "C" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1713 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 14, 'TRANS': 214} Time building chain proxies: 1.89, per 1000 atoms: 0.22 Number of scatterers: 8698 At special positions: 0 Unit cell: (117.432, 91.336, 152.848, 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 34 16.00 O 1688 8.00 N 1452 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 205 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 344.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 23 sheets defined 4.3% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.839A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.540A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.862A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.789A pdb=" N LYS B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.732A pdb=" N GLU B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.520A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.661A pdb=" N LEU A 277 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 273 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 271 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 71 removed outlier: 4.096A pdb=" N HIS A 70 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 78 " --> pdb=" O HIS A 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.811A pdb=" N SER A 117 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 106 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 239 " --> pdb=" O TRP A 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 191 removed outlier: 3.940A pdb=" N LYS A 187 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 189 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 202 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.693A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN A 641 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.623A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 435 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.169A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AB2, first strand: chain 'A' and resid 655 through 659 removed outlier: 4.537A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB4, first strand: chain 'B' and resid 19 through 23 removed outlier: 3.513A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.751A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB7, first strand: chain 'B' and resid 130 through 139 removed outlier: 3.526A pdb=" N ALA B 130 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 132 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 176 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.701A pdb=" N LYS B 145 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 197 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.533A pdb=" N GLN C 5 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 22 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.676A pdb=" N ALA C 91 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 98 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AC3, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.629A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS C 149 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER C 189 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 190 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.629A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS C 152 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU C 187 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR C 154 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL C 178 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 162 through 163 141 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.79 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: 2770 1.34 - 1.46: 2142 1.46 - 1.58: 3969 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 8920 Sorted by residual: bond pdb=" N ILE A 584 " pdb=" CA ILE A 584 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.58e+00 bond pdb=" N LEU A 582 " pdb=" CA LEU A 582 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.31e-02 5.83e+03 6.39e+00 bond pdb=" N GLU A 583 " pdb=" CA GLU A 583 " ideal model delta sigma weight residual 1.461 1.487 -0.026 1.20e-02 6.94e+03 4.73e+00 bond pdb=" N THR A 581 " pdb=" CA THR A 581 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.27e-02 6.20e+03 4.60e+00 bond pdb=" C TYR A 39 " pdb=" N PRO A 40 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.44e-02 4.82e+03 3.53e+00 ... (remaining 8915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11879 1.48 - 2.96: 224 2.96 - 4.44: 35 4.44 - 5.92: 9 5.92 - 7.40: 2 Bond angle restraints: 12149 Sorted by residual: angle pdb=" N TYR A 351 " pdb=" CA TYR A 351 " pdb=" C TYR A 351 " ideal model delta sigma weight residual 114.75 107.35 7.40 1.26e+00 6.30e-01 3.45e+01 angle pdb=" N VAL A 503 " pdb=" CA VAL A 503 " pdb=" C VAL A 503 " ideal model delta sigma weight residual 113.47 109.28 4.19 1.01e+00 9.80e-01 1.72e+01 angle pdb=" C LEU A 582 " pdb=" CA LEU A 582 " pdb=" CB LEU A 582 " ideal model delta sigma weight residual 109.84 116.04 -6.20 1.50e+00 4.44e-01 1.71e+01 angle pdb=" CA TYR A 351 " pdb=" C TYR A 351 " pdb=" N ALA A 352 " ideal model delta sigma weight residual 119.80 115.46 4.34 1.34e+00 5.57e-01 1.05e+01 angle pdb=" N VAL A 350 " pdb=" CA VAL A 350 " pdb=" C VAL A 350 " ideal model delta sigma weight residual 106.21 109.52 -3.31 1.07e+00 8.73e-01 9.57e+00 ... (remaining 12144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 5019 14.09 - 28.19: 198 28.19 - 42.28: 52 42.28 - 56.38: 11 56.38 - 70.47: 6 Dihedral angle restraints: 5286 sinusoidal: 2026 harmonic: 3260 Sorted by residual: dihedral pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" N TYR A 351 " pdb=" CA TYR A 351 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -115.75 29.75 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" C LEU A 582 " pdb=" N LEU A 582 " pdb=" CA LEU A 582 " pdb=" CB LEU A 582 " ideal model delta harmonic sigma weight residual -122.60 -130.40 7.80 0 2.50e+00 1.60e-01 9.75e+00 ... (remaining 5283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1206 0.075 - 0.151: 145 0.151 - 0.226: 3 0.226 - 0.302: 0 0.302 - 0.377: 1 Chirality restraints: 1355 Sorted by residual: chirality pdb=" CG LEU A 582 " pdb=" CB LEU A 582 " pdb=" CD1 LEU A 582 " pdb=" CD2 LEU A 582 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ILE A 584 " pdb=" N ILE A 584 " pdb=" C ILE A 584 " pdb=" CB ILE A 584 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU A 582 " pdb=" N LEU A 582 " pdb=" C LEU A 582 " pdb=" CB LEU A 582 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1352 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 140 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.12e+00 pdb=" N PRO B 141 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO B 80 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 127 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO C 128 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " 0.027 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 905 2.76 - 3.29: 8112 3.29 - 3.83: 13606 3.83 - 4.36: 15743 4.36 - 4.90: 26733 Nonbonded interactions: 65099 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLU A 340 " pdb=" OG SER B 56 " model vdw 2.259 3.040 nonbonded pdb=" O TYR B 49 " pdb=" OG1 THR B 53 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR B 36 " pdb=" NE2 GLN B 89 " model vdw 2.283 3.120 ... (remaining 65094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 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 0.037 8929 Z= 0.122 Angle : 0.520 7.403 12167 Z= 0.310 Chirality : 0.044 0.377 1355 Planarity : 0.004 0.062 1563 Dihedral : 8.535 70.474 3175 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 3.78 % Allowed : 5.82 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.63 (0.21), residues: 1114 helix: -4.23 (0.38), residues: 30 sheet: -2.90 (0.29), residues: 257 loop : -3.35 (0.18), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.005 0.001 TYR C 53 PHE 0.005 0.001 PHE B 139 TRP 0.004 0.001 TRP C 36 HIS 0.001 0.000 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 8920) covalent geometry : angle 0.51995 (12149) SS BOND : bond 0.00086 ( 9) SS BOND : angle 0.41484 ( 18) hydrogen bonds : bond 0.32035 ( 138) hydrogen bonds : angle 11.55081 ( 336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.1587 (OUTLIER) cc_final: 0.1300 (m) REVERT: A 55 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6348 (mt) REVERT: A 60 PHE cc_start: 0.6994 (m-80) cc_final: 0.6412 (m-80) REVERT: A 82 ASN cc_start: 0.6932 (m-40) cc_final: 0.6524 (m-40) REVERT: A 274 THR cc_start: 0.6818 (p) cc_final: 0.6563 (p) REVERT: A 298 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6657 (mt-10) REVERT: A 378 LYS cc_start: 0.7706 (pttm) cc_final: 0.7393 (pttm) REVERT: A 396 TYR cc_start: 0.8387 (m-80) cc_final: 0.7979 (m-10) REVERT: A 406 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7392 (mt-10) REVERT: A 422 ASN cc_start: 0.7320 (m-40) cc_final: 0.7114 (m110) REVERT: A 442 ASP cc_start: 0.6840 (m-30) cc_final: 0.6537 (m-30) REVERT: A 472 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6008 (pt) REVERT: A 547 THR cc_start: 0.7861 (m) cc_final: 0.7599 (p) REVERT: A 556 ASN cc_start: 0.7664 (m-40) cc_final: 0.7310 (m-40) REVERT: A 573 THR cc_start: 0.8783 (m) cc_final: 0.8521 (p) REVERT: A 578 ASP cc_start: 0.7042 (m-30) cc_final: 0.6600 (m-30) REVERT: A 581 THR cc_start: 0.8308 (p) cc_final: 0.7930 (p) REVERT: A 583 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6253 (mt-10) REVERT: A 584 ILE cc_start: 0.4816 (OUTLIER) cc_final: 0.4557 (pt) REVERT: A 612 TYR cc_start: 0.7081 (m-80) cc_final: 0.6253 (m-80) REVERT: A 624 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6481 (pt) REVERT: A 643 PHE cc_start: 0.5231 (m-80) cc_final: 0.4791 (m-80) REVERT: A 645 THR cc_start: 0.6690 (p) cc_final: 0.6006 (t) REVERT: B 107 LYS cc_start: 0.8417 (mtmp) cc_final: 0.8151 (ptpp) REVERT: B 108 ARG cc_start: 0.7005 (mmt90) cc_final: 0.6663 (mmt90) REVERT: B 123 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7923 (mt-10) REVERT: B 148 TRP cc_start: 0.5480 (OUTLIER) cc_final: 0.5202 (m100) REVERT: B 177 SER cc_start: 0.7074 (m) cc_final: 0.6574 (p) REVERT: B 179 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5975 (tm) REVERT: C 75 LYS cc_start: 0.8650 (ptmt) cc_final: 0.7849 (ptpp) REVERT: C 78 PHE cc_start: 0.7710 (p90) cc_final: 0.7452 (p90) REVERT: C 84 SER cc_start: 0.7689 (p) cc_final: 0.7172 (p) REVERT: C 92 VAL cc_start: 0.8236 (t) cc_final: 0.7682 (p) REVERT: C 179 LEU cc_start: 0.7936 (mt) cc_final: 0.7718 (mt) REVERT: C 220 VAL cc_start: 0.7528 (t) cc_final: 0.6978 (p) outliers start: 37 outliers final: 17 residues processed: 300 average time/residue: 0.0901 time to fit residues: 36.3417 Evaluate side-chains 253 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 149 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 62 ASN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 135 GLN A 185 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS A 641 ASN B 6 GLN B 27 GLN B 38 GLN B 89 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN C 58 ASN C 60 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.201681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.169911 restraints weight = 15643.891| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 4.03 r_work: 0.4014 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8929 Z= 0.164 Angle : 0.632 9.466 12167 Z= 0.317 Chirality : 0.047 0.176 1355 Planarity : 0.005 0.060 1563 Dihedral : 7.078 75.169 1262 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.61 % Favored : 90.31 % Rotamer: Outliers : 4.39 % Allowed : 12.97 % Favored : 82.64 % 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 aren not related in a simple way. whole: -4.07 (0.22), residues: 1114 helix: -4.11 (0.43), residues: 31 sheet: -2.37 (0.27), residues: 301 loop : -2.98 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.018 0.002 TYR A 313 PHE 0.023 0.002 PHE B 118 TRP 0.011 0.001 TRP C 34 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8920) covalent geometry : angle 0.63011 (12149) SS BOND : bond 0.00383 ( 9) SS BOND : angle 1.27179 ( 18) hydrogen bonds : bond 0.04284 ( 138) hydrogen bonds : angle 7.79825 ( 336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.3035 (OUTLIER) cc_final: 0.2766 (m) REVERT: A 55 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6944 (mt) REVERT: A 60 PHE cc_start: 0.7324 (m-80) cc_final: 0.6727 (m-80) REVERT: A 62 ASN cc_start: 0.7035 (m110) cc_final: 0.6826 (m-40) REVERT: A 82 ASN cc_start: 0.7138 (m-40) cc_final: 0.6896 (m-40) REVERT: A 202 LYS cc_start: 0.5881 (mttt) cc_final: 0.4934 (mtmm) REVERT: A 317 ASN cc_start: 0.6636 (m110) cc_final: 0.6380 (m110) REVERT: A 355 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7444 (ttt180) REVERT: A 360 ASN cc_start: 0.8045 (m-40) cc_final: 0.7836 (m-40) REVERT: A 382 VAL cc_start: 0.8372 (t) cc_final: 0.8045 (p) REVERT: A 396 TYR cc_start: 0.8487 (m-80) cc_final: 0.8055 (m-10) REVERT: A 422 ASN cc_start: 0.8054 (m-40) cc_final: 0.7802 (m110) REVERT: A 434 ILE cc_start: 0.8650 (mp) cc_final: 0.8372 (mt) REVERT: A 472 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6251 (pt) REVERT: A 487 ASN cc_start: 0.7897 (m-40) cc_final: 0.7592 (m-40) REVERT: A 509 ARG cc_start: 0.7332 (mtt180) cc_final: 0.6918 (mmt90) REVERT: A 556 ASN cc_start: 0.8026 (m-40) cc_final: 0.7724 (m-40) REVERT: A 562 PHE cc_start: 0.7330 (m-10) cc_final: 0.6940 (m-80) REVERT: A 578 ASP cc_start: 0.7966 (m-30) cc_final: 0.7497 (m-30) REVERT: A 583 GLU cc_start: 0.7859 (mt-10) cc_final: 0.6976 (mt-10) REVERT: A 584 ILE cc_start: 0.5780 (OUTLIER) cc_final: 0.5400 (pt) REVERT: A 586 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: A 612 TYR cc_start: 0.7372 (m-80) cc_final: 0.6375 (m-80) REVERT: A 624 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6755 (pt) REVERT: A 628 GLN cc_start: 0.6399 (mp10) cc_final: 0.5961 (mp10) REVERT: A 643 PHE cc_start: 0.5985 (m-80) cc_final: 0.5455 (m-80) REVERT: A 676 THR cc_start: 0.7702 (m) cc_final: 0.7489 (t) REVERT: B 24 ARG cc_start: 0.7888 (mtp-110) cc_final: 0.7402 (mtp85) REVERT: B 108 ARG cc_start: 0.7817 (mmt90) cc_final: 0.7384 (mmt90) REVERT: B 123 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8062 (mt-10) REVERT: B 147 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6591 (tm-30) REVERT: B 177 SER cc_start: 0.7685 (m) cc_final: 0.7431 (p) REVERT: C 33 TYR cc_start: 0.8044 (m-80) cc_final: 0.7672 (m-80) REVERT: C 54 THR cc_start: 0.8434 (p) cc_final: 0.8150 (t) REVERT: C 75 LYS cc_start: 0.8834 (ptmt) cc_final: 0.8169 (ptpp) REVERT: C 78 PHE cc_start: 0.8354 (p90) cc_final: 0.8077 (p90) REVERT: C 109 MET cc_start: 0.8245 (mmt) cc_final: 0.7853 (mtm) REVERT: C 201 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7296 (tm-30) outliers start: 43 outliers final: 23 residues processed: 279 average time/residue: 0.0921 time to fit residues: 35.0772 Evaluate side-chains 280 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 58 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.195824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.163565 restraints weight = 15266.441| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 3.90 r_work: 0.3947 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 8929 Z= 0.200 Angle : 0.690 18.845 12167 Z= 0.349 Chirality : 0.049 0.389 1355 Planarity : 0.005 0.064 1563 Dihedral : 6.550 58.588 1248 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.59 % Favored : 89.32 % Rotamer: Outliers : 5.62 % Allowed : 15.02 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.70 (0.22), residues: 1114 helix: -3.74 (0.60), residues: 31 sheet: -1.99 (0.29), residues: 292 loop : -2.78 (0.19), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 273 TYR 0.016 0.002 TYR C 50 PHE 0.017 0.002 PHE A 56 TRP 0.024 0.002 TRP C 34 HIS 0.007 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8920) covalent geometry : angle 0.67988 (12149) SS BOND : bond 0.00829 ( 9) SS BOND : angle 3.14025 ( 18) hydrogen bonds : bond 0.04234 ( 138) hydrogen bonds : angle 7.14338 ( 336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6874 (mt) REVERT: A 57 LEU cc_start: 0.7865 (mt) cc_final: 0.7273 (mm) REVERT: A 60 PHE cc_start: 0.7314 (m-80) cc_final: 0.6676 (m-80) REVERT: A 62 ASN cc_start: 0.7374 (m-40) cc_final: 0.6927 (m-40) REVERT: A 82 ASN cc_start: 0.7093 (m-40) cc_final: 0.6768 (m-40) REVERT: A 202 LYS cc_start: 0.6120 (mttt) cc_final: 0.5245 (mtmt) REVERT: A 320 VAL cc_start: 0.7795 (m) cc_final: 0.7104 (p) REVERT: A 349 SER cc_start: 0.8727 (m) cc_final: 0.8218 (p) REVERT: A 355 ARG cc_start: 0.7723 (ttt180) cc_final: 0.7364 (ttt180) REVERT: A 396 TYR cc_start: 0.8539 (m-80) cc_final: 0.8086 (m-10) REVERT: A 402 ILE cc_start: 0.7586 (tp) cc_final: 0.7220 (tt) REVERT: A 422 ASN cc_start: 0.8075 (m-40) cc_final: 0.7870 (m110) REVERT: A 434 ILE cc_start: 0.8683 (mp) cc_final: 0.8402 (mt) REVERT: A 472 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.6306 (pt) REVERT: A 523 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7829 (p) REVERT: A 556 ASN cc_start: 0.7986 (m-40) cc_final: 0.7716 (m-40) REVERT: A 565 PHE cc_start: 0.7044 (t80) cc_final: 0.6752 (t80) REVERT: A 583 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 586 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: A 612 TYR cc_start: 0.7603 (m-80) cc_final: 0.6481 (m-80) REVERT: A 627 ASP cc_start: 0.5488 (p0) cc_final: 0.4969 (p0) REVERT: A 643 PHE cc_start: 0.5891 (m-80) cc_final: 0.5410 (m-80) REVERT: A 656 VAL cc_start: 0.7108 (t) cc_final: 0.6831 (p) REVERT: B 74 THR cc_start: 0.8155 (m) cc_final: 0.7927 (t) REVERT: B 108 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7459 (mmt90) REVERT: B 147 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6464 (tm-30) REVERT: C 11 LEU cc_start: 0.8016 (mt) cc_final: 0.7798 (tp) REVERT: C 75 LYS cc_start: 0.8871 (ptmt) cc_final: 0.8418 (ptpp) REVERT: C 109 MET cc_start: 0.8143 (mmt) cc_final: 0.7740 (mtm) REVERT: C 120 VAL cc_start: 0.8632 (t) cc_final: 0.8425 (m) outliers start: 55 outliers final: 30 residues processed: 278 average time/residue: 0.0938 time to fit residues: 35.5730 Evaluate side-chains 263 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 23 optimal weight: 40.0000 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 58 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.195914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.163752 restraints weight = 15631.842| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.98 r_work: 0.3948 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8929 Z= 0.146 Angle : 0.658 11.979 12167 Z= 0.329 Chirality : 0.047 0.272 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.272 59.725 1244 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.14 % Favored : 89.77 % Rotamer: Outliers : 5.11 % Allowed : 17.36 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.23), residues: 1114 helix: -3.32 (0.74), residues: 31 sheet: -1.87 (0.30), residues: 297 loop : -2.67 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 24 TYR 0.018 0.001 TYR C 50 PHE 0.023 0.001 PHE A 497 TRP 0.020 0.001 TRP C 34 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8920) covalent geometry : angle 0.65202 (12149) SS BOND : bond 0.00368 ( 9) SS BOND : angle 2.45992 ( 18) hydrogen bonds : bond 0.03632 ( 138) hydrogen bonds : angle 6.60281 ( 336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7033 (mm) REVERT: A 60 PHE cc_start: 0.7250 (m-80) cc_final: 0.6647 (m-80) REVERT: A 82 ASN cc_start: 0.7071 (m-40) cc_final: 0.6705 (m-40) REVERT: A 98 LYS cc_start: 0.7223 (mtmm) cc_final: 0.6923 (mppt) REVERT: A 349 SER cc_start: 0.8718 (m) cc_final: 0.8471 (m) REVERT: A 355 ARG cc_start: 0.7747 (ttt180) cc_final: 0.7301 (ttt180) REVERT: A 396 TYR cc_start: 0.8480 (m-80) cc_final: 0.7832 (m-10) REVERT: A 402 ILE cc_start: 0.7430 (tp) cc_final: 0.7077 (tt) REVERT: A 434 ILE cc_start: 0.8632 (mp) cc_final: 0.8363 (mt) REVERT: A 472 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.6312 (pt) REVERT: A 478 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8608 (tptp) REVERT: A 509 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6893 (mmt90) REVERT: A 516 GLU cc_start: 0.7867 (tt0) cc_final: 0.7504 (tt0) REVERT: A 523 THR cc_start: 0.8256 (p) cc_final: 0.7949 (p) REVERT: A 552 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7307 (mt) REVERT: A 556 ASN cc_start: 0.7928 (m-40) cc_final: 0.7693 (m-40) REVERT: A 565 PHE cc_start: 0.7043 (t80) cc_final: 0.6724 (t80) REVERT: A 583 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 586 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: A 612 TYR cc_start: 0.7686 (m-80) cc_final: 0.6583 (m-80) REVERT: A 624 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7273 (pt) REVERT: A 627 ASP cc_start: 0.5515 (p0) cc_final: 0.4713 (p0) REVERT: A 629 LEU cc_start: 0.7776 (mm) cc_final: 0.7312 (mt) REVERT: A 643 PHE cc_start: 0.5846 (m-80) cc_final: 0.5474 (m-80) REVERT: A 649 CYS cc_start: 0.7450 (m) cc_final: 0.7213 (m) REVERT: A 656 VAL cc_start: 0.7181 (t) cc_final: 0.6877 (p) REVERT: B 74 THR cc_start: 0.8130 (m) cc_final: 0.7919 (t) REVERT: B 108 ARG cc_start: 0.7878 (mmt90) cc_final: 0.7543 (mmt90) REVERT: B 147 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6740 (tm-30) REVERT: C 75 LYS cc_start: 0.8860 (ptmt) cc_final: 0.8201 (ptpp) REVERT: C 77 GLN cc_start: 0.8470 (pt0) cc_final: 0.8267 (pt0) REVERT: C 120 VAL cc_start: 0.8569 (t) cc_final: 0.8354 (m) outliers start: 50 outliers final: 34 residues processed: 267 average time/residue: 0.0987 time to fit residues: 35.2200 Evaluate side-chains 262 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.196505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164287 restraints weight = 15635.612| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 4.00 r_work: 0.3948 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8929 Z= 0.130 Angle : 0.662 15.345 12167 Z= 0.324 Chirality : 0.047 0.301 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.000 55.085 1242 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.50 % Favored : 89.41 % Rotamer: Outliers : 5.31 % Allowed : 17.26 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.23), residues: 1114 helix: -3.41 (0.68), residues: 36 sheet: -1.76 (0.29), residues: 303 loop : -2.60 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.018 0.001 TYR C 50 PHE 0.020 0.001 PHE A 497 TRP 0.018 0.001 TRP C 34 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8920) covalent geometry : angle 0.65468 (12149) SS BOND : bond 0.00622 ( 9) SS BOND : angle 2.55946 ( 18) hydrogen bonds : bond 0.03383 ( 138) hydrogen bonds : angle 6.19044 ( 336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7088 (mm) REVERT: A 60 PHE cc_start: 0.7261 (m-80) cc_final: 0.6745 (m-80) REVERT: A 62 ASN cc_start: 0.7334 (m-40) cc_final: 0.6936 (m-40) REVERT: A 82 ASN cc_start: 0.7081 (m-40) cc_final: 0.6705 (m-40) REVERT: A 98 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6862 (mppt) REVERT: A 266 TYR cc_start: 0.3193 (m-10) cc_final: 0.2406 (m-10) REVERT: A 355 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7438 (ttt180) REVERT: A 402 ILE cc_start: 0.7371 (tp) cc_final: 0.6989 (tt) REVERT: A 420 ASP cc_start: 0.7487 (t70) cc_final: 0.7078 (t0) REVERT: A 434 ILE cc_start: 0.8590 (mp) cc_final: 0.8387 (mt) REVERT: A 451 TYR cc_start: 0.8349 (m-10) cc_final: 0.7907 (m-80) REVERT: A 455 LEU cc_start: 0.8297 (tp) cc_final: 0.8031 (tt) REVERT: A 472 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6396 (pt) REVERT: A 509 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6957 (mmt90) REVERT: A 516 GLU cc_start: 0.7812 (tt0) cc_final: 0.7542 (tt0) REVERT: A 523 THR cc_start: 0.8215 (p) cc_final: 0.7900 (p) REVERT: A 552 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7495 (mt) REVERT: A 565 PHE cc_start: 0.7023 (t80) cc_final: 0.6700 (t80) REVERT: A 583 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 586 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: A 612 TYR cc_start: 0.7700 (m-80) cc_final: 0.6645 (m-80) REVERT: A 627 ASP cc_start: 0.5079 (p0) cc_final: 0.4315 (p0) REVERT: A 629 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7254 (mt) REVERT: A 643 PHE cc_start: 0.5839 (m-80) cc_final: 0.5449 (m-80) REVERT: A 649 CYS cc_start: 0.7360 (m) cc_final: 0.6700 (t) REVERT: A 656 VAL cc_start: 0.7135 (t) cc_final: 0.6822 (p) REVERT: B 74 THR cc_start: 0.8139 (m) cc_final: 0.7929 (t) REVERT: B 108 ARG cc_start: 0.7855 (mmt90) cc_final: 0.7532 (mmt90) REVERT: B 147 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6795 (tm-30) REVERT: C 57 THR cc_start: 0.8323 (p) cc_final: 0.7999 (t) REVERT: C 75 LYS cc_start: 0.8821 (ptmt) cc_final: 0.8342 (ptpp) REVERT: C 77 GLN cc_start: 0.8481 (pt0) cc_final: 0.8272 (pt0) outliers start: 52 outliers final: 39 residues processed: 261 average time/residue: 0.1023 time to fit residues: 35.6762 Evaluate side-chains 263 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.192137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160550 restraints weight = 15513.742| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.87 r_work: 0.3907 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8929 Z= 0.173 Angle : 0.706 16.715 12167 Z= 0.353 Chirality : 0.049 0.341 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.209 53.890 1242 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.49 % Favored : 88.33 % Rotamer: Outliers : 5.41 % Allowed : 18.69 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.33 (0.23), residues: 1114 helix: -3.48 (0.67), residues: 36 sheet: -1.69 (0.29), residues: 305 loop : -2.53 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 466 TYR 0.017 0.001 TYR C 50 PHE 0.027 0.002 PHE B 118 TRP 0.025 0.001 TRP C 34 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8920) covalent geometry : angle 0.69403 (12149) SS BOND : bond 0.00582 ( 9) SS BOND : angle 3.43305 ( 18) hydrogen bonds : bond 0.04077 ( 138) hydrogen bonds : angle 6.24368 ( 336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.7826 (mt0) cc_final: 0.7484 (mt0) REVERT: A 57 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7329 (mm) REVERT: A 60 PHE cc_start: 0.7175 (m-80) cc_final: 0.6730 (m-80) REVERT: A 62 ASN cc_start: 0.7499 (m-40) cc_final: 0.7086 (m-40) REVERT: A 82 ASN cc_start: 0.7261 (m-40) cc_final: 0.6847 (m-40) REVERT: A 98 LYS cc_start: 0.7281 (mtmm) cc_final: 0.6939 (mppt) REVERT: A 303 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7604 (pp) REVERT: A 320 VAL cc_start: 0.7732 (m) cc_final: 0.7033 (p) REVERT: A 355 ARG cc_start: 0.7767 (ttt180) cc_final: 0.7464 (ttt180) REVERT: A 378 LYS cc_start: 0.7546 (pttm) cc_final: 0.7324 (pttm) REVERT: A 402 ILE cc_start: 0.7555 (tp) cc_final: 0.7179 (tt) REVERT: A 451 TYR cc_start: 0.8397 (m-10) cc_final: 0.8081 (m-80) REVERT: A 455 LEU cc_start: 0.8366 (tp) cc_final: 0.8098 (tt) REVERT: A 516 GLU cc_start: 0.7746 (tt0) cc_final: 0.7465 (tt0) REVERT: A 523 THR cc_start: 0.8219 (p) cc_final: 0.7892 (p) REVERT: A 565 PHE cc_start: 0.7039 (t80) cc_final: 0.6799 (t80) REVERT: A 578 ASP cc_start: 0.8064 (m-30) cc_final: 0.7719 (m-30) REVERT: A 583 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 586 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: A 612 TYR cc_start: 0.7774 (m-80) cc_final: 0.6707 (m-80) REVERT: A 627 ASP cc_start: 0.5300 (p0) cc_final: 0.4409 (p0) REVERT: A 629 LEU cc_start: 0.7758 (mm) cc_final: 0.7359 (mt) REVERT: A 643 PHE cc_start: 0.5884 (m-80) cc_final: 0.5504 (m-80) REVERT: A 656 VAL cc_start: 0.7227 (t) cc_final: 0.6896 (p) REVERT: B 108 ARG cc_start: 0.7885 (mmt90) cc_final: 0.7559 (mmt90) REVERT: B 147 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6620 (tm-30) REVERT: B 179 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6857 (tm) REVERT: C 57 THR cc_start: 0.8424 (p) cc_final: 0.8172 (t) REVERT: C 75 LYS cc_start: 0.8800 (ptmt) cc_final: 0.8318 (ptpp) REVERT: C 77 GLN cc_start: 0.8554 (pt0) cc_final: 0.8346 (pt0) REVERT: C 92 VAL cc_start: 0.8552 (t) cc_final: 0.8220 (p) REVERT: C 99 TYR cc_start: 0.8423 (t80) cc_final: 0.8197 (t80) REVERT: C 187 LEU cc_start: 0.7893 (pp) cc_final: 0.7518 (pt) outliers start: 53 outliers final: 40 residues processed: 270 average time/residue: 0.0996 time to fit residues: 35.8292 Evaluate side-chains 280 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 556 ASN B 27 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.192821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.160786 restraints weight = 15728.715| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.99 r_work: 0.3919 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8929 Z= 0.133 Angle : 0.695 16.475 12167 Z= 0.343 Chirality : 0.048 0.325 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.041 53.914 1239 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.50 % Favored : 89.41 % Rotamer: Outliers : 5.52 % Allowed : 19.31 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.23), residues: 1114 helix: -3.32 (0.76), residues: 30 sheet: -1.52 (0.29), residues: 305 loop : -2.43 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.031 0.001 TYR C 53 PHE 0.023 0.001 PHE B 118 TRP 0.021 0.001 TRP C 34 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8920) covalent geometry : angle 0.68268 (12149) SS BOND : bond 0.00601 ( 9) SS BOND : angle 3.49461 ( 18) hydrogen bonds : bond 0.03761 ( 138) hydrogen bonds : angle 6.09463 ( 336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5343 (tp) REVERT: A 53 GLN cc_start: 0.7740 (mt0) cc_final: 0.7372 (mt0) REVERT: A 57 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.6778 (mm) REVERT: A 60 PHE cc_start: 0.7152 (m-80) cc_final: 0.6661 (m-80) REVERT: A 82 ASN cc_start: 0.7240 (m-40) cc_final: 0.6801 (m-40) REVERT: A 98 LYS cc_start: 0.7272 (mtmm) cc_final: 0.6874 (mppt) REVERT: A 266 TYR cc_start: 0.3925 (m-10) cc_final: 0.3141 (m-10) REVERT: A 273 ARG cc_start: 0.7393 (mtt180) cc_final: 0.7088 (mtt180) REVERT: A 303 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7630 (pp) REVERT: A 355 ARG cc_start: 0.7779 (ttt180) cc_final: 0.7428 (ttt180) REVERT: A 378 LYS cc_start: 0.7586 (pttm) cc_final: 0.7284 (pttm) REVERT: A 402 ILE cc_start: 0.7384 (tp) cc_final: 0.6997 (tt) REVERT: A 420 ASP cc_start: 0.7565 (t70) cc_final: 0.7169 (t0) REVERT: A 434 ILE cc_start: 0.8599 (mp) cc_final: 0.8331 (mt) REVERT: A 451 TYR cc_start: 0.8377 (m-10) cc_final: 0.7975 (m-80) REVERT: A 455 LEU cc_start: 0.8356 (tp) cc_final: 0.8089 (tt) REVERT: A 509 ARG cc_start: 0.7412 (mtt180) cc_final: 0.7016 (mmt90) REVERT: A 523 THR cc_start: 0.8203 (p) cc_final: 0.7869 (p) REVERT: A 565 PHE cc_start: 0.7040 (t80) cc_final: 0.6699 (t80) REVERT: A 577 ARG cc_start: 0.8016 (ttt90) cc_final: 0.7804 (ttt90) REVERT: A 583 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 586 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: A 612 TYR cc_start: 0.7756 (m-80) cc_final: 0.6664 (m-80) REVERT: A 627 ASP cc_start: 0.5258 (p0) cc_final: 0.4432 (p0) REVERT: A 629 LEU cc_start: 0.7746 (mm) cc_final: 0.7321 (mt) REVERT: A 643 PHE cc_start: 0.5989 (m-80) cc_final: 0.5491 (m-80) REVERT: A 656 VAL cc_start: 0.7192 (t) cc_final: 0.6851 (p) REVERT: B 9 SER cc_start: 0.8156 (m) cc_final: 0.7849 (p) REVERT: B 27 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8330 (tp40) REVERT: B 108 ARG cc_start: 0.7887 (mmt90) cc_final: 0.7550 (mmt90) REVERT: B 147 GLN cc_start: 0.6926 (tm-30) cc_final: 0.6637 (tm-30) REVERT: B 179 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6826 (tm) REVERT: B 181 LEU cc_start: 0.8391 (mt) cc_final: 0.8051 (tp) REVERT: C 35 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7431 (p) REVERT: C 57 THR cc_start: 0.8396 (p) cc_final: 0.8150 (t) REVERT: C 75 LYS cc_start: 0.8765 (ptmt) cc_final: 0.8461 (ptpp) REVERT: C 77 GLN cc_start: 0.8537 (pt0) cc_final: 0.8326 (pt0) REVERT: C 99 TYR cc_start: 0.8384 (t80) cc_final: 0.8170 (t80) REVERT: C 133 LEU cc_start: 0.5074 (OUTLIER) cc_final: 0.4452 (pp) outliers start: 54 outliers final: 37 residues processed: 274 average time/residue: 0.0992 time to fit residues: 36.3091 Evaluate side-chains 289 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 chunk 107 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 27 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.192119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.159904 restraints weight = 15411.727| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.93 r_work: 0.3906 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8929 Z= 0.158 Angle : 0.711 17.171 12167 Z= 0.353 Chirality : 0.048 0.329 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.017 54.861 1237 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.67 % Favored : 88.15 % Rotamer: Outliers : 5.31 % Allowed : 20.33 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.24), residues: 1114 helix: -3.37 (0.70), residues: 35 sheet: -1.43 (0.29), residues: 309 loop : -2.45 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 454 TYR 0.031 0.001 TYR C 53 PHE 0.019 0.001 PHE B 118 TRP 0.023 0.001 TRP C 34 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8920) covalent geometry : angle 0.69746 (12149) SS BOND : bond 0.00765 ( 9) SS BOND : angle 3.62033 ( 18) hydrogen bonds : bond 0.03814 ( 138) hydrogen bonds : angle 6.10667 ( 336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.7883 (mt0) cc_final: 0.7486 (mt0) REVERT: A 57 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.6965 (mm) REVERT: A 60 PHE cc_start: 0.7150 (m-80) cc_final: 0.6672 (m-80) REVERT: A 62 ASN cc_start: 0.7676 (m-40) cc_final: 0.7141 (m-40) REVERT: A 82 ASN cc_start: 0.7305 (m-40) cc_final: 0.7059 (m110) REVERT: A 98 LYS cc_start: 0.7439 (mtmm) cc_final: 0.7013 (mppt) REVERT: A 266 TYR cc_start: 0.3749 (m-10) cc_final: 0.3542 (m-10) REVERT: A 271 GLN cc_start: 0.7309 (mm-40) cc_final: 0.7091 (mm-40) REVERT: A 273 ARG cc_start: 0.7299 (mtt180) cc_final: 0.7026 (mtt180) REVERT: A 317 ASN cc_start: 0.6894 (t0) cc_final: 0.6420 (m-40) REVERT: A 320 VAL cc_start: 0.7724 (m) cc_final: 0.7040 (p) REVERT: A 355 ARG cc_start: 0.7780 (ttt180) cc_final: 0.7479 (ttt180) REVERT: A 378 LYS cc_start: 0.7632 (pttm) cc_final: 0.7392 (pttm) REVERT: A 392 PHE cc_start: 0.7590 (m-80) cc_final: 0.7147 (m-80) REVERT: A 402 ILE cc_start: 0.7439 (tp) cc_final: 0.7044 (tt) REVERT: A 434 ILE cc_start: 0.8633 (mp) cc_final: 0.8380 (mt) REVERT: A 451 TYR cc_start: 0.8390 (m-10) cc_final: 0.8054 (m-80) REVERT: A 455 LEU cc_start: 0.8326 (tp) cc_final: 0.8090 (tt) REVERT: A 478 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8640 (tptp) REVERT: A 509 ARG cc_start: 0.7409 (mtt180) cc_final: 0.6979 (mmt90) REVERT: A 523 THR cc_start: 0.8152 (p) cc_final: 0.7839 (p) REVERT: A 565 PHE cc_start: 0.7064 (t80) cc_final: 0.6713 (t80) REVERT: A 577 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7834 (ttt90) REVERT: A 578 ASP cc_start: 0.8097 (m-30) cc_final: 0.7657 (m-30) REVERT: A 583 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7410 (mt-10) REVERT: A 586 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: A 612 TYR cc_start: 0.7763 (m-80) cc_final: 0.6694 (m-80) REVERT: A 627 ASP cc_start: 0.5498 (p0) cc_final: 0.4638 (p0) REVERT: A 629 LEU cc_start: 0.7748 (mm) cc_final: 0.7346 (mt) REVERT: A 641 ASN cc_start: 0.5774 (m110) cc_final: 0.4793 (m-40) REVERT: A 654 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6750 (mm-30) REVERT: A 656 VAL cc_start: 0.7200 (t) cc_final: 0.6861 (p) REVERT: B 9 SER cc_start: 0.8162 (m) cc_final: 0.7866 (p) REVERT: B 67 SER cc_start: 0.8428 (t) cc_final: 0.8077 (p) REVERT: B 108 ARG cc_start: 0.7914 (mmt90) cc_final: 0.7586 (mmt90) REVERT: B 179 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6867 (tm) REVERT: B 181 LEU cc_start: 0.8422 (mt) cc_final: 0.8074 (tp) REVERT: C 35 THR cc_start: 0.8065 (p) cc_final: 0.7731 (p) REVERT: C 38 ARG cc_start: 0.8848 (ttp-170) cc_final: 0.8535 (mtp180) REVERT: C 57 THR cc_start: 0.8449 (p) cc_final: 0.8189 (t) REVERT: C 75 LYS cc_start: 0.8803 (ptmt) cc_final: 0.8492 (ptpp) REVERT: C 99 TYR cc_start: 0.8376 (t80) cc_final: 0.8163 (t80) REVERT: C 133 LEU cc_start: 0.5151 (OUTLIER) cc_final: 0.4488 (pp) REVERT: C 187 LEU cc_start: 0.7869 (pp) cc_final: 0.7499 (pt) outliers start: 52 outliers final: 39 residues processed: 279 average time/residue: 0.1009 time to fit residues: 37.5158 Evaluate side-chains 291 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.0000 chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 540 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.191469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.159012 restraints weight = 15345.683| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.97 r_work: 0.3903 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8929 Z= 0.148 Angle : 0.721 18.188 12167 Z= 0.357 Chirality : 0.048 0.332 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.023 54.773 1237 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.86 % Favored : 88.96 % Rotamer: Outliers : 5.01 % Allowed : 20.63 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.24), residues: 1114 helix: -3.46 (0.67), residues: 35 sheet: -1.33 (0.29), residues: 306 loop : -2.42 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.031 0.001 TYR C 53 PHE 0.021 0.001 PHE B 118 TRP 0.025 0.001 TRP C 34 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8920) covalent geometry : angle 0.70773 (12149) SS BOND : bond 0.00686 ( 9) SS BOND : angle 3.63184 ( 18) hydrogen bonds : bond 0.03746 ( 138) hydrogen bonds : angle 6.01443 ( 336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.6993 (mm) REVERT: A 60 PHE cc_start: 0.7167 (m-80) cc_final: 0.6659 (m-80) REVERT: A 98 LYS cc_start: 0.7366 (mtmm) cc_final: 0.6906 (mppt) REVERT: A 266 TYR cc_start: 0.3757 (m-10) cc_final: 0.3542 (m-10) REVERT: A 273 ARG cc_start: 0.7312 (mtt180) cc_final: 0.6999 (mtt180) REVERT: A 317 ASN cc_start: 0.6863 (t0) cc_final: 0.6412 (m-40) REVERT: A 320 VAL cc_start: 0.7717 (m) cc_final: 0.7001 (p) REVERT: A 355 ARG cc_start: 0.7794 (ttt180) cc_final: 0.7459 (ttt180) REVERT: A 378 LYS cc_start: 0.7662 (pttm) cc_final: 0.7410 (pttm) REVERT: A 392 PHE cc_start: 0.7585 (m-80) cc_final: 0.7190 (m-80) REVERT: A 402 ILE cc_start: 0.7355 (tp) cc_final: 0.6986 (tt) REVERT: A 422 ASN cc_start: 0.7872 (m-40) cc_final: 0.7444 (m-40) REVERT: A 434 ILE cc_start: 0.8622 (mp) cc_final: 0.8382 (mt) REVERT: A 451 TYR cc_start: 0.8406 (m-10) cc_final: 0.8040 (m-80) REVERT: A 455 LEU cc_start: 0.8353 (tp) cc_final: 0.8111 (tt) REVERT: A 509 ARG cc_start: 0.7410 (mtt180) cc_final: 0.6970 (mmt90) REVERT: A 523 THR cc_start: 0.8139 (p) cc_final: 0.7845 (p) REVERT: A 565 PHE cc_start: 0.7107 (t80) cc_final: 0.6787 (t80) REVERT: A 578 ASP cc_start: 0.8083 (m-30) cc_final: 0.7856 (m-30) REVERT: A 586 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: A 612 TYR cc_start: 0.7810 (m-80) cc_final: 0.6756 (m-80) REVERT: A 627 ASP cc_start: 0.5475 (p0) cc_final: 0.4685 (p0) REVERT: A 629 LEU cc_start: 0.7776 (mm) cc_final: 0.7367 (mt) REVERT: A 656 VAL cc_start: 0.7285 (t) cc_final: 0.6933 (p) REVERT: B 9 SER cc_start: 0.8152 (m) cc_final: 0.7839 (p) REVERT: B 108 ARG cc_start: 0.7920 (mmt90) cc_final: 0.7583 (mmt90) REVERT: B 179 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6838 (tm) REVERT: B 181 LEU cc_start: 0.8454 (mt) cc_final: 0.8100 (tp) REVERT: C 32 TYR cc_start: 0.8245 (m-10) cc_final: 0.7948 (m-80) REVERT: C 35 THR cc_start: 0.8191 (p) cc_final: 0.7938 (p) REVERT: C 38 ARG cc_start: 0.8865 (ttp-170) cc_final: 0.8575 (mtp180) REVERT: C 43 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8314 (mtmt) REVERT: C 57 THR cc_start: 0.8488 (p) cc_final: 0.8210 (t) REVERT: C 75 LYS cc_start: 0.8809 (ptmt) cc_final: 0.8526 (ptpp) REVERT: C 99 TYR cc_start: 0.8389 (t80) cc_final: 0.8187 (t80) outliers start: 49 outliers final: 42 residues processed: 267 average time/residue: 0.1071 time to fit residues: 37.9378 Evaluate side-chains 282 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 0.0020 chunk 2 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** 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 = 0.4467 r_free = 0.4467 target = 0.193619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.161891 restraints weight = 15664.020| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 3.95 r_work: 0.3944 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8929 Z= 0.117 Angle : 0.714 18.626 12167 Z= 0.351 Chirality : 0.048 0.326 1355 Planarity : 0.005 0.062 1563 Dihedral : 5.853 54.588 1237 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.77 % Favored : 89.14 % Rotamer: Outliers : 4.49 % Allowed : 20.74 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.91 (0.24), residues: 1114 helix: -3.48 (0.66), residues: 35 sheet: -1.14 (0.29), residues: 311 loop : -2.35 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 577 TYR 0.029 0.001 TYR C 53 PHE 0.018 0.001 PHE B 118 TRP 0.019 0.001 TRP C 34 HIS 0.002 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8920) covalent geometry : angle 0.70159 (12149) SS BOND : bond 0.00461 ( 9) SS BOND : angle 3.52003 ( 18) hydrogen bonds : bond 0.03555 ( 138) hydrogen bonds : angle 5.87465 ( 336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7974 (mt) cc_final: 0.6756 (mm) REVERT: A 60 PHE cc_start: 0.7074 (m-80) cc_final: 0.6621 (m-80) REVERT: A 98 LYS cc_start: 0.7519 (mtmm) cc_final: 0.7092 (mppt) REVERT: A 266 TYR cc_start: 0.3647 (m-10) cc_final: 0.2715 (m-10) REVERT: A 317 ASN cc_start: 0.6758 (t0) cc_final: 0.6332 (m-40) REVERT: A 355 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7394 (ttt180) REVERT: A 378 LYS cc_start: 0.7632 (pttm) cc_final: 0.7394 (pttm) REVERT: A 402 ILE cc_start: 0.7231 (tp) cc_final: 0.6923 (tt) REVERT: A 420 ASP cc_start: 0.7540 (t70) cc_final: 0.7138 (t0) REVERT: A 422 ASN cc_start: 0.7782 (m-40) cc_final: 0.7359 (m-40) REVERT: A 434 ILE cc_start: 0.8534 (mp) cc_final: 0.8289 (mt) REVERT: A 451 TYR cc_start: 0.8356 (m-10) cc_final: 0.8013 (m-80) REVERT: A 455 LEU cc_start: 0.8308 (tp) cc_final: 0.8085 (tt) REVERT: A 509 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7010 (mmt90) REVERT: A 523 THR cc_start: 0.8070 (p) cc_final: 0.7760 (p) REVERT: A 565 PHE cc_start: 0.6984 (t80) cc_final: 0.6637 (t80) REVERT: A 586 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: A 612 TYR cc_start: 0.7741 (m-80) cc_final: 0.6962 (m-80) REVERT: A 627 ASP cc_start: 0.5262 (p0) cc_final: 0.4520 (p0) REVERT: A 629 LEU cc_start: 0.7746 (mm) cc_final: 0.7413 (mp) REVERT: A 656 VAL cc_start: 0.7281 (t) cc_final: 0.6938 (p) REVERT: B 9 SER cc_start: 0.8110 (m) cc_final: 0.7788 (p) REVERT: B 108 ARG cc_start: 0.7895 (mmt90) cc_final: 0.7568 (mmt90) REVERT: B 179 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6752 (tm) REVERT: B 181 LEU cc_start: 0.8472 (mt) cc_final: 0.8116 (tp) REVERT: C 35 THR cc_start: 0.8183 (p) cc_final: 0.7895 (p) REVERT: C 38 ARG cc_start: 0.8797 (ttp-170) cc_final: 0.8535 (mtp180) REVERT: C 43 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8284 (mtmt) REVERT: C 57 THR cc_start: 0.8438 (p) cc_final: 0.8181 (t) REVERT: C 75 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8484 (ptpp) REVERT: C 109 MET cc_start: 0.8263 (mmt) cc_final: 0.7874 (mtm) outliers start: 44 outliers final: 40 residues processed: 261 average time/residue: 0.1097 time to fit residues: 38.1331 Evaluate side-chains 278 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 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 = 0.4448 r_free = 0.4448 target = 0.192532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.160084 restraints weight = 15338.835| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 4.00 r_work: 0.3908 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8929 Z= 0.160 Angle : 0.753 18.267 12167 Z= 0.371 Chirality : 0.049 0.316 1355 Planarity : 0.005 0.063 1563 Dihedral : 5.893 54.838 1235 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.12 % Favored : 87.70 % Rotamer: Outliers : 4.80 % Allowed : 20.84 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.24), residues: 1114 helix: -3.54 (0.60), residues: 41 sheet: -1.20 (0.29), residues: 318 loop : -2.32 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 357 TYR 0.030 0.001 TYR C 53 PHE 0.017 0.001 PHE B 118 TRP 0.034 0.002 TRP B 148 HIS 0.006 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8920) covalent geometry : angle 0.73987 (12149) SS BOND : bond 0.00721 ( 9) SS BOND : angle 3.67787 ( 18) hydrogen bonds : bond 0.03713 ( 138) hydrogen bonds : angle 5.97245 ( 336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2395.48 seconds wall clock time: 41 minutes 45.15 seconds (2505.15 seconds total)