Starting phenix.real_space_refine on Mon Jul 28 17:40:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gy2_34368/07_2025/8gy2_34368.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gy2_34368/07_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_34368/07_2025/8gy2_34368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gy2_34368/07_2025/8gy2_34368.map" model { file = "/net/cci-nas-00/data/ceres_data/8gy2_34368/07_2025/8gy2_34368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gy2_34368/07_2025/8gy2_34368.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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-8': 1, 'U10:plan-9': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 7.22, per 1000 atoms: 0.73 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: 2.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.11 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: 3.35 Time building geometry restraints manager: 2.89 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: 2.660 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.730 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:14.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- 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 : 7.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP A 331 HIS 0.002 0.000 HIS A 362 PHE 0.008 0.001 PHE C 100 TYR 0.010 0.001 TYR A 593 ARG 0.001 0.000 ARG B 171 Details of bonding type rmsd hydrogen bonds : bond 0.14067 ( 333) hydrogen bonds : angle 7.82820 ( 897) SS BOND : bond 0.00496 ( 2) SS BOND : angle 1.09828 ( 4) covalent geometry : bond 0.00743 (10257) covalent geometry : angle 0.66759 (14033) 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 : 1.026 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: 1.3750 time to fit residues: 148.8665 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 : 1.266 ------------------------------------------------------------------------------- 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 105 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.068968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.055613 restraints weight = 19675.987| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.18 r_work: 0.2563 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0549 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= 0.182 Angle : 0.641 12.366 14037 Z= 0.310 Chirality : 0.046 0.155 1412 Planarity : 0.004 0.046 1834 Dihedral : 10.588 101.052 1461 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.18 % Allowed : 20.38 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1258 helix: 1.28 (0.32), residues: 289 sheet: -0.12 (0.41), residues: 151 loop : -0.66 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 585 HIS 0.004 0.001 HIS B 92 PHE 0.009 0.001 PHE A 383 TYR 0.014 0.001 TYR A 593 ARG 0.002 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 333) hydrogen bonds : angle 6.29350 ( 897) SS BOND : bond 0.00393 ( 2) SS BOND : angle 1.48141 ( 4) covalent geometry : bond 0.00449 (10257) covalent geometry : angle 0.64056 (14033) Misc. bond : bond 0.08879 ( 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 104 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8662 (p0) cc_final: 0.8337 (t0) REVERT: B 394 MET cc_start: 0.8955 (ttt) cc_final: 0.8165 (ttt) outliers start: 32 outliers final: 22 residues processed: 96 average time/residue: 1.6277 time to fit residues: 171.8819 Evaluate side-chains 92 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 644 ASP 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 Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.070351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.057334 restraints weight = 19909.082| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 2.13 r_work: 0.2562 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 10272 Z= 0.127 Angle : 0.588 9.966 14037 Z= 0.287 Chirality : 0.045 0.150 1412 Planarity : 0.004 0.042 1834 Dihedral : 10.171 101.473 1443 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1258 helix: 1.27 (0.31), residues: 293 sheet: -0.12 (0.40), residues: 151 loop : -0.62 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.003 0.001 HIS B 92 PHE 0.009 0.001 PHE C 100 TYR 0.011 0.001 TYR A 593 ARG 0.002 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 333) hydrogen bonds : angle 5.87572 ( 897) SS BOND : bond 0.00519 ( 2) SS BOND : angle 1.50706 ( 4) covalent geometry : bond 0.00312 (10257) covalent geometry : angle 0.58735 (14033) Misc. bond : bond 0.07245 ( 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 109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8647 (p0) cc_final: 0.8395 (t0) REVERT: A 740 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8358 (mp-120) REVERT: B 84 THR cc_start: 0.8609 (m) cc_final: 0.8351 (p) REVERT: B 277 MET cc_start: 0.9215 (tpt) cc_final: 0.7152 (tpt) REVERT: B 394 MET cc_start: 0.8876 (ttt) cc_final: 0.8209 (ttt) outliers start: 33 outliers final: 16 residues processed: 102 average time/residue: 1.1611 time to fit residues: 128.7782 Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 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 110 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 116 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 103 ASN C 123 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.070720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.057286 restraints weight = 19605.056| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 2.19 r_work: 0.2567 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 10272 Z= 0.120 Angle : 0.581 9.246 14037 Z= 0.284 Chirality : 0.044 0.149 1412 Planarity : 0.004 0.039 1834 Dihedral : 9.937 100.846 1440 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.88 % Allowed : 20.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1258 helix: 1.26 (0.31), residues: 299 sheet: -0.16 (0.41), residues: 151 loop : -0.62 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS A 756 PHE 0.009 0.001 PHE C 100 TYR 0.011 0.001 TYR A 593 ARG 0.002 0.000 ARG A 730 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 333) hydrogen bonds : angle 5.70953 ( 897) SS BOND : bond 0.00539 ( 2) SS BOND : angle 1.49981 ( 4) covalent geometry : bond 0.00296 (10257) covalent geometry : angle 0.58071 (14033) Misc. bond : bond 0.06727 ( 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 104 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8620 (p0) cc_final: 0.8409 (t0) REVERT: B 84 THR cc_start: 0.8620 (m) cc_final: 0.8376 (p) REVERT: B 100 GLU cc_start: 0.8595 (tp30) cc_final: 0.8395 (tp30) outliers start: 29 outliers final: 16 residues processed: 97 average time/residue: 1.3930 time to fit residues: 146.3345 Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 223 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.2924 r_free = 0.2924 target = 0.069611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.056358 restraints weight = 19570.393| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 2.16 r_work: 0.2584 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 10272 Z= 0.171 Angle : 0.628 14.140 14037 Z= 0.301 Chirality : 0.046 0.153 1412 Planarity : 0.004 0.041 1834 Dihedral : 9.987 101.104 1438 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.98 % Allowed : 21.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1258 helix: 1.33 (0.32), residues: 293 sheet: -0.18 (0.41), residues: 151 loop : -0.64 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 585 HIS 0.003 0.001 HIS A 756 PHE 0.009 0.001 PHE A 383 TYR 0.015 0.001 TYR A 329 ARG 0.002 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 333) hydrogen bonds : angle 5.79428 ( 897) SS BOND : bond 0.00440 ( 2) SS BOND : angle 1.62719 ( 4) covalent geometry : bond 0.00423 (10257) covalent geometry : angle 0.62736 (14033) Misc. bond : bond 0.08120 ( 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 101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8140 (t0) cc_final: 0.7865 (t0) REVERT: B 84 THR cc_start: 0.8656 (m) cc_final: 0.8433 (p) REVERT: B 100 GLU cc_start: 0.8608 (tp30) cc_final: 0.8348 (tp30) REVERT: B 318 GLN cc_start: 0.8393 (mt0) cc_final: 0.8076 (mt0) REVERT: B 394 MET cc_start: 0.9162 (ttt) cc_final: 0.8710 (ttt) outliers start: 30 outliers final: 19 residues processed: 96 average time/residue: 1.2447 time to fit residues: 129.3563 Evaluate side-chains 88 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 223 SER 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 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 Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.2923 r_free = 0.2923 target = 0.069681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.056255 restraints weight = 19684.216| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.18 r_work: 0.2559 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 10272 Z= 0.132 Angle : 0.599 12.371 14037 Z= 0.290 Chirality : 0.045 0.146 1412 Planarity : 0.004 0.039 1834 Dihedral : 9.932 102.059 1438 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.39 % Allowed : 22.17 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1258 helix: 1.38 (0.31), residues: 293 sheet: -0.17 (0.41), residues: 151 loop : -0.63 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.003 0.001 HIS B 92 PHE 0.008 0.001 PHE C 100 TYR 0.012 0.001 TYR A 593 ARG 0.001 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 333) hydrogen bonds : angle 5.69721 ( 897) SS BOND : bond 0.00513 ( 2) SS BOND : angle 1.54346 ( 4) covalent geometry : bond 0.00325 (10257) covalent geometry : angle 0.59862 (14033) Misc. bond : bond 0.07365 ( 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: 24 poor density : 71 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8065 (t0) cc_final: 0.7806 (t0) REVERT: B 84 THR cc_start: 0.8625 (m) cc_final: 0.8386 (p) REVERT: B 100 GLU cc_start: 0.8627 (tp30) cc_final: 0.8351 (tp30) REVERT: B 178 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.9113 (mtp) REVERT: B 318 GLN cc_start: 0.8366 (mt0) cc_final: 0.8045 (mt0) REVERT: B 394 MET cc_start: 0.9078 (ttt) cc_final: 0.8517 (ttt) outliers start: 24 outliers final: 18 residues processed: 91 average time/residue: 1.6809 time to fit residues: 170.0147 Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 2.837 ------------------------------------------------------------------------------- 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 223 SER 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 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 115 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 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 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.070182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.056713 restraints weight = 19884.809| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.20 r_work: 0.2576 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1165 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= 0.124 Angle : 0.590 11.711 14037 Z= 0.285 Chirality : 0.044 0.145 1412 Planarity : 0.004 0.038 1834 Dihedral : 9.844 101.841 1438 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.29 % Allowed : 22.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1258 helix: 1.35 (0.31), residues: 298 sheet: -0.16 (0.41), residues: 150 loop : -0.60 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.004 0.001 HIS B 92 PHE 0.009 0.001 PHE C 100 TYR 0.011 0.001 TYR A 593 ARG 0.001 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 333) hydrogen bonds : angle 5.63462 ( 897) SS BOND : bond 0.00530 ( 2) SS BOND : angle 1.54847 ( 4) covalent geometry : bond 0.00305 (10257) covalent geometry : angle 0.58939 (14033) Misc. bond : bond 0.07150 ( 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 95 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8116 (t0) cc_final: 0.7814 (t0) REVERT: B 84 THR cc_start: 0.8624 (m) cc_final: 0.8405 (p) REVERT: B 100 GLU cc_start: 0.8631 (tp30) cc_final: 0.8361 (tp30) REVERT: B 178 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.9116 (mtp) REVERT: B 318 GLN cc_start: 0.8384 (mt0) cc_final: 0.8061 (mt0) REVERT: B 394 MET cc_start: 0.9064 (ttt) cc_final: 0.8456 (ttt) REVERT: C 115 GLU cc_start: 0.8792 (tt0) cc_final: 0.8562 (tt0) outliers start: 23 outliers final: 19 residues processed: 91 average time/residue: 1.5803 time to fit residues: 155.9939 Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 223 SER 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 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 124 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.2930 r_free = 0.2930 target = 0.070078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.056640 restraints weight = 19730.538| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.20 r_work: 0.2575 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 10272 Z= 0.126 Angle : 0.589 11.439 14037 Z= 0.283 Chirality : 0.044 0.144 1412 Planarity : 0.004 0.038 1834 Dihedral : 9.820 101.702 1437 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.39 % Allowed : 22.17 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1258 helix: 1.37 (0.31), residues: 298 sheet: -0.15 (0.42), residues: 150 loop : -0.60 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.004 0.001 HIS B 92 PHE 0.008 0.001 PHE C 100 TYR 0.012 0.001 TYR A 593 ARG 0.001 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 333) hydrogen bonds : angle 5.60567 ( 897) SS BOND : bond 0.00526 ( 2) SS BOND : angle 1.55588 ( 4) covalent geometry : bond 0.00309 (10257) covalent geometry : angle 0.58858 (14033) Misc. bond : bond 0.07740 ( 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 94 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8103 (t0) cc_final: 0.7787 (t0) REVERT: A 228 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: B 84 THR cc_start: 0.8633 (m) cc_final: 0.8417 (p) REVERT: B 100 GLU cc_start: 0.8631 (tp30) cc_final: 0.8362 (tp30) REVERT: B 178 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9138 (mtp) REVERT: B 318 GLN cc_start: 0.8394 (mt0) cc_final: 0.8067 (mt0) REVERT: B 394 MET cc_start: 0.9050 (ttt) cc_final: 0.8481 (ttt) REVERT: C 115 GLU cc_start: 0.8808 (tt0) cc_final: 0.8561 (tt0) outliers start: 24 outliers final: 19 residues processed: 89 average time/residue: 1.3593 time to fit residues: 131.4534 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 : 1.069 ------------------------------------------------------------------------------- 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 223 SER Chi-restraints excluded: chain A residue 228 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 47 SER 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 48 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 HIS B 270 HIS C 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.067928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.054466 restraints weight = 19910.119| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.18 r_work: 0.2528 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2424 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 10272 Z= 0.196 Angle : 0.654 13.089 14037 Z= 0.314 Chirality : 0.047 0.158 1412 Planarity : 0.004 0.039 1834 Dihedral : 10.020 102.046 1437 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.19 % Allowed : 22.27 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1258 helix: 1.42 (0.32), residues: 289 sheet: -0.20 (0.41), residues: 151 loop : -0.64 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 585 HIS 0.004 0.001 HIS B 92 PHE 0.010 0.001 PHE A 383 TYR 0.017 0.001 TYR A 329 ARG 0.002 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 333) hydrogen bonds : angle 5.78394 ( 897) SS BOND : bond 0.00405 ( 2) SS BOND : angle 1.66492 ( 4) covalent geometry : bond 0.00487 (10257) covalent geometry : angle 0.65330 (14033) Misc. bond : bond 0.09085 ( 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: 22 poor density : 68 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8137 (t0) cc_final: 0.7801 (t0) REVERT: A 228 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: B 84 THR cc_start: 0.8682 (m) cc_final: 0.8412 (p) REVERT: B 100 GLU cc_start: 0.8655 (tp30) cc_final: 0.8330 (tp30) REVERT: B 318 GLN cc_start: 0.8419 (mt0) cc_final: 0.8061 (mt0) outliers start: 22 outliers final: 17 residues processed: 86 average time/residue: 1.1969 time to fit residues: 111.7395 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 : 1.172 ------------------------------------------------------------------------------- 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 223 SER Chi-restraints excluded: chain A residue 228 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.2940 r_free = 0.2940 target = 0.070623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.057144 restraints weight = 19722.178| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 2.20 r_work: 0.2564 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 10272 Z= 0.113 Angle : 0.585 12.221 14037 Z= 0.280 Chirality : 0.044 0.145 1412 Planarity : 0.004 0.038 1834 Dihedral : 9.892 103.418 1437 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.79 % Allowed : 22.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1258 helix: 1.38 (0.31), residues: 297 sheet: -0.14 (0.41), residues: 151 loop : -0.61 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.003 0.000 HIS B 92 PHE 0.010 0.001 PHE C 100 TYR 0.010 0.001 TYR A 547 ARG 0.001 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 333) hydrogen bonds : angle 5.59555 ( 897) SS BOND : bond 0.00583 ( 2) SS BOND : angle 1.56202 ( 4) covalent geometry : bond 0.00272 (10257) covalent geometry : angle 0.58484 (14033) Misc. bond : bond 0.08907 ( 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: 18 poor density : 70 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8079 (t0) cc_final: 0.7758 (t0) REVERT: B 84 THR cc_start: 0.8654 (m) cc_final: 0.8439 (p) REVERT: B 100 GLU cc_start: 0.8646 (tp30) cc_final: 0.8324 (tp30) REVERT: B 178 MET cc_start: 0.9332 (mtp) cc_final: 0.9055 (mtp) REVERT: B 310 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8790 (mtmm) REVERT: B 318 GLN cc_start: 0.8418 (mt0) cc_final: 0.8056 (mt0) outliers start: 18 outliers final: 16 residues processed: 87 average time/residue: 1.1158 time to fit residues: 105.9025 Evaluate side-chains 84 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 223 SER 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 306 VAL Chi-restraints excluded: chain B residue 310 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.0270 chunk 67 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.2942 r_free = 0.2942 target = 0.070726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.057271 restraints weight = 19576.503| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.19 r_work: 0.2567 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 10272 Z= 0.112 Angle : 0.598 14.996 14037 Z= 0.280 Chirality : 0.044 0.144 1412 Planarity : 0.004 0.039 1834 Dihedral : 9.777 102.415 1437 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1258 helix: 1.47 (0.32), residues: 294 sheet: -0.16 (0.42), residues: 150 loop : -0.57 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 331 HIS 0.003 0.000 HIS B 92 PHE 0.009 0.001 PHE C 100 TYR 0.010 0.001 TYR A 593 ARG 0.001 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 333) hydrogen bonds : angle 5.53148 ( 897) SS BOND : bond 0.00585 ( 2) SS BOND : angle 1.55019 ( 4) covalent geometry : bond 0.00269 (10257) covalent geometry : angle 0.59784 (14033) Misc. bond : bond 0.09385 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7315.90 seconds wall clock time: 133 minutes 42.76 seconds (8022.76 seconds total)