Starting phenix.real_space_refine on Sat Aug 23 07:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gy2_34368/08_2025/8gy2_34368.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gy2_34368/08_2025/8gy2_34368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gy2_34368/08_2025/8gy2_34368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gy2_34368/08_2025/8gy2_34368.map" model { file = "/net/cci-nas-00/data/ceres_data/8gy2_34368/08_2025/8gy2_34368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gy2_34368/08_2025/8gy2_34368.cif" } resolution = 2.5 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 S 44 5.16 5 C 6347 2.51 5 N 1674 2.21 5 O 1873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 9943 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5621 Classifications: {'peptide': 723} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 676} Chain: "B" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3264 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 98} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {' CA': 1, 'HEC': 1, 'PQQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 165 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 2.36, per 1000 atoms: 0.24 Number of scatterers: 9943 At special positions: 0 Unit cell: (73.95, 87, 130.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 44 16.00 O 1873 8.00 N 1674 7.00 C 6347 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 122 " 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=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 387.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 15 sheets defined 32.7% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.846A pdb=" N ILE A 136 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 137 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASP A 138 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 485 through 498 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.754A pdb=" N GLY A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 641 through 653 Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 659 through 662 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 674 through 677 Processing helix chain 'A' and resid 678 through 687 Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 704 through 731 removed outlier: 5.113A pdb=" N ASP A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ASP A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 55 through 60 removed outlier: 4.226A pdb=" N CYS B 59 " --> pdb=" O ASP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 130 through 144 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 164 through 175 removed outlier: 4.291A pdb=" N GLY B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.832A pdb=" N ASP B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 289 through 302 Processing helix chain 'B' and resid 317 through 326 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 402 through 415 Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.510A pdb=" N THR B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.704A pdb=" N VAL B 447 " --> pdb=" O GLY B 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 69 through 80 removed outlier: 4.013A pdb=" N GLY C 75 " --> pdb=" O PRO C 71 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 removed outlier: 4.151A pdb=" N ALA C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 removed outlier: 4.291A pdb=" N VAL A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASP A 548 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP A 554 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 87 removed outlier: 5.053A pdb=" N LEU A 82 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER A 613 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 6.225A pdb=" N ASP A 118 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 124 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.580A pdb=" N LEU A 165 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 178 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA A 167 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 removed outlier: 5.923A pdb=" N ASP A 226 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 232 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 274 through 275 removed outlier: 3.617A pdb=" N GLY A 274 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 282 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 356 removed outlier: 5.989A pdb=" N ASP A 377 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 383 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 395 through 398 removed outlier: 5.093A pdb=" N ASN A 406 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 420 through 422 Processing sheet with id=AB2, first strand: chain 'A' and resid 436 through 438 removed outlier: 7.616A pdb=" N GLY A 501 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN A 518 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 503 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR A 516 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 505 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB4, first strand: chain 'B' and resid 267 through 268 removed outlier: 3.549A pdb=" N SER B 271 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 380 through 382 Processing sheet with id=AB6, first strand: chain 'C' and resid 99 through 101 333 hydrogen bonds defined for protein. 897 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: 1.76 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 3409 1.37 - 1.53: 6392 1.53 - 1.69: 364 1.69 - 1.85: 76 1.85 - 2.01: 16 Bond restraints: 10257 Sorted by residual: bond pdb=" C2D HEC A 801 " pdb=" C3D HEC A 801 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C2D HEC B 502 " pdb=" C3D HEC B 502 " ideal model delta sigma weight residual 1.544 1.328 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2D HEC B 503 " pdb=" C3D HEC B 503 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC B 501 " pdb=" C3D HEC B 501 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CAC HEC B 503 " pdb=" CBC HEC B 503 " ideal model delta sigma weight residual 1.544 1.359 0.185 2.00e-02 2.50e+03 8.55e+01 ... (remaining 10252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 13853 2.76 - 5.53: 165 5.53 - 8.29: 12 8.29 - 11.06: 2 11.06 - 13.82: 1 Bond angle restraints: 14033 Sorted by residual: angle pdb=" C3D HEC B 502 " pdb=" CAD HEC B 502 " pdb=" CBD HEC B 502 " ideal model delta sigma weight residual 109.50 123.32 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" CA GLU A 36 " pdb=" CB GLU A 36 " pdb=" CG GLU A 36 " ideal model delta sigma weight residual 114.10 121.46 -7.36 2.00e+00 2.50e-01 1.36e+01 angle pdb=" C3D HEC B 503 " pdb=" CAD HEC B 503 " pdb=" CBD HEC B 503 " ideal model delta sigma weight residual 109.50 119.18 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C3D HEC B 501 " pdb=" CAD HEC B 501 " pdb=" CBD HEC B 501 " ideal model delta sigma weight residual 109.50 118.14 -8.64 3.00e+00 1.11e-01 8.29e+00 angle pdb=" C VAL A 101 " pdb=" N ASN A 102 " pdb=" CA ASN A 102 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.90e+00 ... (remaining 14028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.25: 5193 20.25 - 40.49: 540 40.49 - 60.74: 113 60.74 - 80.98: 21 80.98 - 101.23: 7 Dihedral angle restraints: 5874 sinusoidal: 2307 harmonic: 3567 Sorted by residual: dihedral pdb=" C16 U10 B 504 " pdb=" C17 U10 B 504 " pdb=" C18 U10 B 504 " pdb=" C19 U10 B 504 " ideal model delta sinusoidal sigma weight residual 199.79 98.56 101.23 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N CYS A 142 " pdb=" CA CYS A 142 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ALA B 393 " pdb=" C ALA B 393 " pdb=" N MET B 394 " pdb=" CA MET B 394 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 792 0.029 - 0.059: 391 0.059 - 0.088: 135 0.088 - 0.117: 74 0.117 - 0.146: 20 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA ILE A 349 " pdb=" N ILE A 349 " pdb=" C ILE A 349 " pdb=" CB ILE A 349 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ASN A 102 " pdb=" N ASN A 102 " pdb=" C ASN A 102 " pdb=" CB ASN A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE A 423 " pdb=" N ILE A 423 " pdb=" C ILE A 423 " pdb=" CB ILE A 423 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1409 not shown) Planarity restraints: 1834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A PQQ A 802 " 0.002 2.00e-02 2.50e+03 2.94e-02 3.90e+01 pdb=" C2 PQQ A 802 " 0.014 2.00e-02 2.50e+03 pdb=" C2X PQQ A 802 " 0.031 2.00e-02 2.50e+03 pdb=" C3 PQQ A 802 " -0.005 2.00e-02 2.50e+03 pdb=" C3A PQQ A 802 " -0.013 2.00e-02 2.50e+03 pdb=" C4 PQQ A 802 " -0.031 2.00e-02 2.50e+03 pdb=" C5 PQQ A 802 " 0.026 2.00e-02 2.50e+03 pdb=" C6A PQQ A 802 " 0.013 2.00e-02 2.50e+03 pdb=" C7 PQQ A 802 " -0.001 2.00e-02 2.50e+03 pdb=" C7X PQQ A 802 " -0.012 2.00e-02 2.50e+03 pdb=" C8 PQQ A 802 " -0.013 2.00e-02 2.50e+03 pdb=" C9 PQQ A 802 " -0.016 2.00e-02 2.50e+03 pdb=" C9A PQQ A 802 " 0.001 2.00e-02 2.50e+03 pdb=" C9X PQQ A 802 " -0.025 2.00e-02 2.50e+03 pdb=" N1 PQQ A 802 " 0.019 2.00e-02 2.50e+03 pdb=" N6 PQQ A 802 " 0.020 2.00e-02 2.50e+03 pdb=" O4 PQQ A 802 " -0.077 2.00e-02 2.50e+03 pdb=" O5 PQQ A 802 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC B 502 " -0.027 2.00e-02 2.50e+03 5.84e-02 3.41e+01 pdb=" CGD HEC B 502 " 0.101 2.00e-02 2.50e+03 pdb=" O1D HEC B 502 " -0.036 2.00e-02 2.50e+03 pdb=" O2D HEC B 502 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC B 503 " -0.024 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" CGD HEC B 503 " 0.090 2.00e-02 2.50e+03 pdb=" O1D HEC B 503 " -0.033 2.00e-02 2.50e+03 pdb=" O2D HEC B 503 " -0.034 2.00e-02 2.50e+03 ... (remaining 1831 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 33 2.39 - 3.02: 5719 3.02 - 3.64: 15365 3.64 - 4.27: 25260 4.27 - 4.90: 41043 Nonbonded interactions: 87420 Sorted by model distance: nonbonded pdb=" O ASP A 342 " pdb=" OD1 ASP A 342 " model vdw 1.759 3.040 nonbonded pdb=" OE1 GLU B 91 " pdb=" NE2 HIS B 92 " model vdw 1.897 3.120 nonbonded pdb=" OE1 GLU B 91 " pdb=" CD2 HIS B 92 " model vdw 2.012 3.260 nonbonded pdb=" N1 PQQ A 802 " pdb=" O9B PQQ A 802 " model vdw 2.116 3.120 nonbonded pdb=" OD2 ASP A 342 " pdb=" O5 PQQ A 802 " model vdw 2.154 3.040 ... (remaining 87415 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.008 0.217 10272 Z= 0.341 Angle : 0.668 13.820 14037 Z= 0.314 Chirality : 0.043 0.146 1412 Planarity : 0.005 0.058 1834 Dihedral : 17.176 101.226 3622 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.88 % Allowed : 21.87 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.26 (0.24), residues: 1258 helix: 1.17 (0.32), residues: 292 sheet: -0.18 (0.41), residues: 152 loop : -0.68 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 171 TYR 0.010 0.001 TYR A 593 PHE 0.008 0.001 PHE C 100 TRP 0.012 0.001 TRP A 331 HIS 0.002 0.000 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00743 (10257) covalent geometry : angle 0.66759 (14033) SS BOND : bond 0.00496 ( 2) SS BOND : angle 1.09828 ( 4) hydrogen bonds : bond 0.14067 ( 333) hydrogen bonds : angle 7.82820 ( 897) Misc. bond : bond 0.04797 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.9067 (tpt) cc_final: 0.7857 (tpt) outliers start: 29 outliers final: 28 residues processed: 100 average time/residue: 0.5893 time to fit residues: 63.6964 Evaluate side-chains 100 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN B 152 ASN B 270 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.069618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.056260 restraints weight = 19732.495| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.19 r_work: 0.2575 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 10272 Z= 0.159 Angle : 0.627 11.793 14037 Z= 0.303 Chirality : 0.046 0.153 1412 Planarity : 0.004 0.045 1834 Dihedral : 10.499 101.046 1461 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.28 % Allowed : 20.18 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.17 (0.24), residues: 1258 helix: 1.31 (0.32), residues: 289 sheet: -0.09 (0.41), residues: 151 loop : -0.64 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 677 TYR 0.013 0.001 TYR A 593 PHE 0.009 0.001 PHE A 383 TRP 0.012 0.001 TRP A 585 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00391 (10257) covalent geometry : angle 0.62697 (14033) SS BOND : bond 0.00483 ( 2) SS BOND : angle 1.46805 ( 4) hydrogen bonds : bond 0.04008 ( 333) hydrogen bonds : angle 6.20719 ( 897) Misc. bond : bond 0.08599 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8655 (p0) cc_final: 0.8325 (t0) REVERT: B 277 MET cc_start: 0.9298 (tpt) cc_final: 0.7306 (tpt) REVERT: B 394 MET cc_start: 0.8931 (ttt) cc_final: 0.8484 (ttt) outliers start: 33 outliers final: 19 residues processed: 101 average time/residue: 0.5495 time to fit residues: 60.4404 Evaluate side-chains 92 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 79 optimal weight: 0.0270 chunk 67 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 270 HIS C 123 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.071697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.058232 restraints weight = 19697.224| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 2.21 r_work: 0.2588 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 10272 Z= 0.111 Angle : 0.565 7.966 14037 Z= 0.277 Chirality : 0.044 0.149 1412 Planarity : 0.004 0.040 1834 Dihedral : 10.068 100.736 1443 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.28 % Allowed : 20.08 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.17 (0.24), residues: 1258 helix: 1.22 (0.31), residues: 299 sheet: -0.12 (0.41), residues: 151 loop : -0.62 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 671 TYR 0.010 0.001 TYR A 593 PHE 0.009 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00269 (10257) covalent geometry : angle 0.56465 (14033) SS BOND : bond 0.00564 ( 2) SS BOND : angle 1.49658 ( 4) hydrogen bonds : bond 0.03311 ( 333) hydrogen bonds : angle 5.78382 ( 897) Misc. bond : bond 0.06284 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8198 (t0) cc_final: 0.7959 (t0) REVERT: A 102 ASN cc_start: 0.8638 (p0) cc_final: 0.8371 (t0) REVERT: B 84 THR cc_start: 0.8577 (m) cc_final: 0.8347 (p) REVERT: B 277 MET cc_start: 0.9213 (tpt) cc_final: 0.7163 (tpt) REVERT: B 394 MET cc_start: 0.8766 (ttt) cc_final: 0.8101 (ttt) outliers start: 33 outliers final: 17 residues processed: 104 average time/residue: 0.5252 time to fit residues: 59.5641 Evaluate side-chains 90 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 40 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.058059 restraints weight = 19859.821| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.21 r_work: 0.2583 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 10272 Z= 0.112 Angle : 0.571 8.114 14037 Z= 0.278 Chirality : 0.044 0.148 1412 Planarity : 0.004 0.038 1834 Dihedral : 9.660 100.009 1438 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.58 % Allowed : 21.17 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.11 (0.24), residues: 1258 helix: 1.33 (0.31), residues: 298 sheet: -0.14 (0.41), residues: 151 loop : -0.59 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 730 TYR 0.010 0.001 TYR A 593 PHE 0.008 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS A 756 Details of bonding type rmsd covalent geometry : bond 0.00275 (10257) covalent geometry : angle 0.57015 (14033) SS BOND : bond 0.00565 ( 2) SS BOND : angle 1.49347 ( 4) hydrogen bonds : bond 0.03199 ( 333) hydrogen bonds : angle 5.65422 ( 897) Misc. bond : bond 0.06414 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8158 (t0) cc_final: 0.7930 (t0) REVERT: A 102 ASN cc_start: 0.8637 (p0) cc_final: 0.8406 (t0) REVERT: B 84 THR cc_start: 0.8570 (m) cc_final: 0.8332 (p) REVERT: B 394 MET cc_start: 0.8796 (ttt) cc_final: 0.8243 (ttt) outliers start: 26 outliers final: 15 residues processed: 94 average time/residue: 0.5216 time to fit residues: 53.4020 Evaluate side-chains 87 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 64 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 58 optimal weight: 0.0870 chunk 51 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.072157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.058685 restraints weight = 19807.134| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.21 r_work: 0.2597 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 10272 Z= 0.104 Angle : 0.557 7.140 14037 Z= 0.272 Chirality : 0.043 0.147 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.511 99.489 1437 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.49 % Allowed : 21.17 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.10 (0.24), residues: 1258 helix: 1.39 (0.31), residues: 298 sheet: -0.16 (0.41), residues: 151 loop : -0.60 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 730 TYR 0.009 0.001 TYR A 593 PHE 0.008 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS A 756 Details of bonding type rmsd covalent geometry : bond 0.00255 (10257) covalent geometry : angle 0.55668 (14033) SS BOND : bond 0.00617 ( 2) SS BOND : angle 1.53192 ( 4) hydrogen bonds : bond 0.03043 ( 333) hydrogen bonds : angle 5.55810 ( 897) Misc. bond : bond 0.05423 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8183 (t0) cc_final: 0.7930 (t0) REVERT: A 117 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8343 (mt) REVERT: B 84 THR cc_start: 0.8574 (m) cc_final: 0.8324 (p) REVERT: B 100 GLU cc_start: 0.8595 (tp30) cc_final: 0.8372 (tp30) REVERT: B 394 MET cc_start: 0.8760 (ttt) cc_final: 0.8210 (ttt) outliers start: 25 outliers final: 15 residues processed: 93 average time/residue: 0.4991 time to fit residues: 50.8314 Evaluate side-chains 86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain C residue 64 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.068748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.055388 restraints weight = 20029.610| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 2.18 r_work: 0.2533 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 10272 Z= 0.181 Angle : 0.626 8.732 14037 Z= 0.305 Chirality : 0.046 0.152 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.700 100.092 1436 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.58 % Allowed : 21.47 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.10 (0.24), residues: 1258 helix: 1.40 (0.32), residues: 293 sheet: -0.16 (0.41), residues: 151 loop : -0.59 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 671 TYR 0.015 0.001 TYR A 329 PHE 0.009 0.001 PHE A 383 TRP 0.013 0.001 TRP A 585 HIS 0.004 0.001 HIS A 756 Details of bonding type rmsd covalent geometry : bond 0.00448 (10257) covalent geometry : angle 0.62526 (14033) SS BOND : bond 0.00454 ( 2) SS BOND : angle 1.61853 ( 4) hydrogen bonds : bond 0.03827 ( 333) hydrogen bonds : angle 5.72835 ( 897) Misc. bond : bond 0.07461 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8276 (t0) cc_final: 0.8026 (t0) REVERT: B 84 THR cc_start: 0.8636 (m) cc_final: 0.8401 (p) REVERT: B 100 GLU cc_start: 0.8606 (tp30) cc_final: 0.8334 (tp30) REVERT: B 178 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.9111 (mtp) REVERT: B 318 GLN cc_start: 0.8368 (mt0) cc_final: 0.8043 (mt0) outliers start: 26 outliers final: 17 residues processed: 92 average time/residue: 0.5057 time to fit residues: 50.5392 Evaluate side-chains 86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 66 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.070013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.056636 restraints weight = 19822.281| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 2.19 r_work: 0.2559 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 10272 Z= 0.130 Angle : 0.597 11.592 14037 Z= 0.288 Chirality : 0.044 0.146 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.633 101.325 1436 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.19 % Allowed : 21.67 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.10 (0.24), residues: 1258 helix: 1.36 (0.31), residues: 298 sheet: -0.14 (0.41), residues: 151 loop : -0.60 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 671 TYR 0.011 0.001 TYR A 593 PHE 0.008 0.001 PHE C 90 TRP 0.011 0.001 TRP A 331 HIS 0.006 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00323 (10257) covalent geometry : angle 0.59678 (14033) SS BOND : bond 0.00558 ( 2) SS BOND : angle 1.59509 ( 4) hydrogen bonds : bond 0.03430 ( 333) hydrogen bonds : angle 5.64695 ( 897) Misc. bond : bond 0.07324 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8214 (t0) cc_final: 0.7953 (t0) REVERT: B 84 THR cc_start: 0.8625 (m) cc_final: 0.8403 (p) REVERT: B 100 GLU cc_start: 0.8608 (tp30) cc_final: 0.8318 (tp30) REVERT: B 178 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9109 (mtp) REVERT: B 318 GLN cc_start: 0.8374 (mt0) cc_final: 0.8029 (mt0) outliers start: 22 outliers final: 18 residues processed: 91 average time/residue: 0.5063 time to fit residues: 50.0698 Evaluate side-chains 87 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 44 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.070832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.057474 restraints weight = 19707.509| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.20 r_work: 0.2601 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 10272 Z= 0.114 Angle : 0.591 14.034 14037 Z= 0.280 Chirality : 0.044 0.143 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.529 101.033 1436 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.09 % Allowed : 21.67 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.04 (0.24), residues: 1258 helix: 1.43 (0.31), residues: 298 sheet: -0.14 (0.42), residues: 151 loop : -0.56 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 671 TYR 0.011 0.001 TYR A 593 PHE 0.008 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.006 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00277 (10257) covalent geometry : angle 0.59068 (14033) SS BOND : bond 0.00582 ( 2) SS BOND : angle 1.54353 ( 4) hydrogen bonds : bond 0.03218 ( 333) hydrogen bonds : angle 5.55989 ( 897) Misc. bond : bond 0.08154 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8206 (t0) cc_final: 0.7955 (t0) REVERT: B 84 THR cc_start: 0.8584 (m) cc_final: 0.8335 (p) REVERT: B 100 GLU cc_start: 0.8630 (tp30) cc_final: 0.8337 (tp30) REVERT: B 178 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9095 (mtp) REVERT: B 318 GLN cc_start: 0.8398 (mt0) cc_final: 0.8069 (mt0) outliers start: 21 outliers final: 17 residues processed: 85 average time/residue: 0.4978 time to fit residues: 46.0989 Evaluate side-chains 86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 99 optimal weight: 0.0470 chunk 95 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 120 optimal weight: 0.0050 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.4492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.071846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.058473 restraints weight = 19518.364| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.20 r_work: 0.2622 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 10272 Z= 0.103 Angle : 0.571 12.944 14037 Z= 0.271 Chirality : 0.043 0.144 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.412 100.356 1435 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.99 % Allowed : 21.97 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.01 (0.24), residues: 1258 helix: 1.48 (0.32), residues: 298 sheet: -0.16 (0.42), residues: 151 loop : -0.53 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 671 TYR 0.010 0.001 TYR A 593 PHE 0.009 0.001 PHE C 100 TRP 0.012 0.001 TRP A 331 HIS 0.004 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00249 (10257) covalent geometry : angle 0.57012 (14033) SS BOND : bond 0.00655 ( 2) SS BOND : angle 1.59493 ( 4) hydrogen bonds : bond 0.03045 ( 333) hydrogen bonds : angle 5.47447 ( 897) Misc. bond : bond 0.07386 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8203 (t0) cc_final: 0.7942 (t0) REVERT: B 84 THR cc_start: 0.8598 (m) cc_final: 0.8353 (p) REVERT: B 100 GLU cc_start: 0.8655 (tp30) cc_final: 0.8316 (tp30) REVERT: B 178 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9138 (mtt) REVERT: B 318 GLN cc_start: 0.8391 (mt0) cc_final: 0.8056 (mt0) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.4759 time to fit residues: 44.4713 Evaluate side-chains 84 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 107 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 61 GLN C 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.070918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.057528 restraints weight = 19512.764| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 2.19 r_work: 0.2564 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 10272 Z= 0.125 Angle : 0.603 14.709 14037 Z= 0.284 Chirality : 0.044 0.145 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.420 100.170 1435 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.99 % Allowed : 22.37 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.01 (0.24), residues: 1258 helix: 1.51 (0.32), residues: 294 sheet: -0.17 (0.41), residues: 151 loop : -0.52 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 671 TYR 0.011 0.001 TYR A 593 PHE 0.008 0.001 PHE C 100 TRP 0.010 0.001 TRP A 331 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00306 (10257) covalent geometry : angle 0.60215 (14033) SS BOND : bond 0.00620 ( 2) SS BOND : angle 1.62387 ( 4) hydrogen bonds : bond 0.03281 ( 333) hydrogen bonds : angle 5.50899 ( 897) Misc. bond : bond 0.08472 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8235 (t0) cc_final: 0.7972 (t0) REVERT: B 84 THR cc_start: 0.8618 (m) cc_final: 0.8148 (p) REVERT: B 100 GLU cc_start: 0.8660 (tp30) cc_final: 0.8333 (tp30) REVERT: B 178 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9027 (mtt) REVERT: B 318 GLN cc_start: 0.8390 (mt0) cc_final: 0.8034 (mt0) outliers start: 20 outliers final: 17 residues processed: 84 average time/residue: 0.4779 time to fit residues: 43.8572 Evaluate side-chains 83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 61 GLN C 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.070773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.057360 restraints weight = 19599.100| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.19 r_work: 0.2594 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 10272 Z= 0.126 Angle : 0.605 14.742 14037 Z= 0.283 Chirality : 0.044 0.146 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.435 100.396 1435 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.79 % Allowed : 22.37 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.00 (0.24), residues: 1258 helix: 1.47 (0.32), residues: 297 sheet: -0.15 (0.41), residues: 151 loop : -0.53 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 671 TYR 0.011 0.001 TYR A 593 PHE 0.008 0.001 PHE C 100 TRP 0.010 0.001 TRP A 331 HIS 0.004 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00309 (10257) covalent geometry : angle 0.60495 (14033) SS BOND : bond 0.00619 ( 2) SS BOND : angle 1.64157 ( 4) hydrogen bonds : bond 0.03309 ( 333) hydrogen bonds : angle 5.52152 ( 897) Misc. bond : bond 0.08927 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.70 seconds wall clock time: 55 minutes 13.98 seconds (3313.98 seconds total)