Starting phenix.real_space_refine on Wed Sep 25 14:48:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/09_2024/8gy2_34368.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/09_2024/8gy2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/09_2024/8gy2_34368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/09_2024/8gy2_34368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/09_2024/8gy2_34368.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/09_2024/8gy2_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-5461/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: 6.25, per 1000 atoms: 0.63 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 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: 1.06 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: 2.90 Time building geometry restraints manager: 2.93 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:9.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- 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 : 0.007 0.217 10257 Z= 0.516 Angle : 0.668 13.820 14033 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 *********************** 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 fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 1.138 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: 1.1412 time to fit residues: 123.8079 Evaluate side-chains 100 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 : 0.004 0.056 10257 Z= 0.300 Angle : 0.641 12.367 14033 Z= 0.309 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 *********************** 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 fitting. rotamer outliers: 32 poor density : 72 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8629 (p0) cc_final: 0.8325 (t0) REVERT: B 394 MET cc_start: 0.8947 (ttt) cc_final: 0.8104 (ttt) outliers start: 32 outliers final: 22 residues processed: 96 average time/residue: 1.1423 time to fit residues: 119.5561 Evaluate side-chains 92 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 C 123 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10257 Z= 0.181 Angle : 0.575 9.237 14033 Z= 0.281 Chirality : 0.044 0.147 1412 Planarity : 0.004 0.041 1834 Dihedral : 10.145 101.231 1443 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.28 % Allowed : 20.28 % 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: -0.18 (0.24), residues: 1258 helix: 1.20 (0.31), residues: 299 sheet: -0.11 (0.41), residues: 151 loop : -0.63 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 *********************** 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 110 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 77 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8630 (p0) cc_final: 0.8382 (t0) REVERT: A 740 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8222 (mp-120) REVERT: B 84 THR cc_start: 0.8591 (m) cc_final: 0.8350 (p) REVERT: B 277 MET cc_start: 0.9252 (tpt) cc_final: 0.7217 (tpt) REVERT: B 394 MET cc_start: 0.8867 (ttt) cc_final: 0.8163 (ttt) outliers start: 33 outliers final: 17 residues processed: 103 average time/residue: 1.1751 time to fit residues: 131.8256 Evaluate side-chains 90 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 112 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 108 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10257 Z= 0.239 Angle : 0.598 10.003 14033 Z= 0.292 Chirality : 0.045 0.153 1412 Planarity : 0.004 0.041 1834 Dihedral : 10.019 100.715 1440 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.68 % Allowed : 21.07 % 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: -0.19 (0.24), residues: 1258 helix: 1.22 (0.31), residues: 299 sheet: -0.14 (0.41), residues: 150 loop : -0.64 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 585 HIS 0.003 0.001 HIS A 756 PHE 0.008 0.001 PHE C 100 TYR 0.013 0.001 TYR A 593 ARG 0.002 0.000 ARG A 730 *********************** 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 102 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8602 (p0) cc_final: 0.8387 (t0) REVERT: B 84 THR cc_start: 0.8612 (m) cc_final: 0.8379 (p) REVERT: B 277 MET cc_start: 0.9212 (tpt) cc_final: 0.7253 (tpt) REVERT: B 394 MET cc_start: 0.8906 (ttt) cc_final: 0.8239 (ttt) outliers start: 27 outliers final: 18 residues processed: 96 average time/residue: 1.0777 time to fit residues: 113.1694 Evaluate side-chains 90 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 89 optimal weight: 0.1980 chunk 49 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10257 Z= 0.221 Angle : 0.590 9.161 14033 Z= 0.288 Chirality : 0.045 0.149 1412 Planarity : 0.004 0.040 1834 Dihedral : 9.931 101.144 1439 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.78 % Allowed : 20.87 % 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 (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: 1.26 (0.31), residues: 299 sheet: -0.15 (0.41), residues: 151 loop : -0.63 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.003 0.000 HIS A 756 PHE 0.009 0.001 PHE C 100 TYR 0.012 0.001 TYR A 593 ARG 0.001 0.000 ARG A 671 *********************** 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 fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 THR cc_start: 0.8626 (m) cc_final: 0.8399 (p) REVERT: B 100 GLU cc_start: 0.8401 (tp30) cc_final: 0.8175 (tp30) REVERT: B 318 GLN cc_start: 0.8145 (mt0) cc_final: 0.7815 (mt0) REVERT: B 394 MET cc_start: 0.8899 (ttt) cc_final: 0.8364 (ttt) outliers start: 28 outliers final: 17 residues processed: 96 average time/residue: 1.1501 time to fit residues: 120.1845 Evaluate side-chains 86 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 120 optimal weight: 0.0980 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.0050 chunk 63 optimal weight: 0.0570 chunk 116 optimal weight: 2.9990 overall best weight: 0.2912 ------------------------------------------------------------------------------- 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 61 GLN C 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10257 Z= 0.154 Angle : 0.555 7.405 14033 Z= 0.273 Chirality : 0.043 0.142 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.709 100.435 1438 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.29 % Allowed : 21.97 % Favored : 75.75 % 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: -0.07 (0.24), residues: 1258 helix: 1.39 (0.31), residues: 298 sheet: -0.12 (0.42), residues: 151 loop : -0.58 (0.22), residues: 809 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 0.009 0.001 TYR A 547 ARG 0.001 0.000 ARG A 730 *********************** 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 97 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7606 (t0) REVERT: B 84 THR cc_start: 0.8572 (m) cc_final: 0.8337 (p) REVERT: B 100 GLU cc_start: 0.8423 (tp30) cc_final: 0.8158 (tp30) REVERT: B 318 GLN cc_start: 0.8135 (mt0) cc_final: 0.7791 (mt0) outliers start: 23 outliers final: 15 residues processed: 93 average time/residue: 1.0498 time to fit residues: 107.2004 Evaluate side-chains 86 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10257 Z= 0.309 Angle : 0.641 15.375 14033 Z= 0.304 Chirality : 0.046 0.157 1412 Planarity : 0.004 0.039 1834 Dihedral : 9.652 100.098 1436 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.09 % Allowed : 22.27 % 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: -0.12 (0.24), residues: 1258 helix: 1.34 (0.31), residues: 299 sheet: -0.16 (0.41), residues: 151 loop : -0.60 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 585 HIS 0.005 0.001 HIS B 92 PHE 0.009 0.001 PHE A 383 TYR 0.015 0.001 TYR A 329 ARG 0.002 0.000 ARG A 671 *********************** 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 91 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7869 (t160) cc_final: 0.7579 (t0) REVERT: B 84 THR cc_start: 0.8657 (m) cc_final: 0.8435 (p) REVERT: B 100 GLU cc_start: 0.8456 (tp30) cc_final: 0.8179 (tp30) REVERT: B 178 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.9116 (mtp) REVERT: B 318 GLN cc_start: 0.8171 (mt0) cc_final: 0.7815 (mt0) outliers start: 21 outliers final: 18 residues processed: 89 average time/residue: 1.1440 time to fit residues: 111.0908 Evaluate side-chains 88 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.0270 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10257 Z= 0.201 Angle : 0.601 12.178 14033 Z= 0.289 Chirality : 0.044 0.145 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.609 101.237 1436 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.29 % Allowed : 21.87 % 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: -0.09 (0.24), residues: 1258 helix: 1.38 (0.31), residues: 298 sheet: -0.17 (0.41), residues: 151 loop : -0.59 (0.22), residues: 809 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 730 *********************** 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 93 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7823 (t160) cc_final: 0.7548 (t0) REVERT: B 84 THR cc_start: 0.8614 (m) cc_final: 0.8402 (p) REVERT: B 100 GLU cc_start: 0.8432 (tp30) cc_final: 0.8154 (tp30) REVERT: B 178 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9103 (mtp) REVERT: B 318 GLN cc_start: 0.8177 (mt0) cc_final: 0.7796 (mt0) outliers start: 23 outliers final: 18 residues processed: 90 average time/residue: 1.1183 time to fit residues: 109.7426 Evaluate side-chains 87 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 112 optimal weight: 0.9980 chunk 115 optimal weight: 0.0570 chunk 67 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10257 Z= 0.168 Angle : 0.582 13.857 14033 Z= 0.275 Chirality : 0.043 0.142 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.463 100.899 1435 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.19 % Allowed : 21.97 % 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: -0.04 (0.24), residues: 1258 helix: 1.45 (0.31), residues: 297 sheet: -0.16 (0.42), residues: 151 loop : -0.56 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 331 HIS 0.004 0.000 HIS B 92 PHE 0.009 0.001 PHE C 100 TYR 0.010 0.001 TYR A 593 ARG 0.002 0.000 ARG B 353 *********************** 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 91 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7807 (t160) cc_final: 0.7470 (t0) REVERT: B 84 THR cc_start: 0.8595 (m) cc_final: 0.8360 (p) REVERT: B 100 GLU cc_start: 0.8480 (tp30) cc_final: 0.8206 (tp30) REVERT: B 178 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.9103 (mtp) REVERT: B 318 GLN cc_start: 0.8192 (mt0) cc_final: 0.7827 (mt0) outliers start: 22 outliers final: 17 residues processed: 88 average time/residue: 1.1203 time to fit residues: 107.6070 Evaluate side-chains 86 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 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 72 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10257 Z= 0.200 Angle : 0.606 14.723 14033 Z= 0.284 Chirality : 0.044 0.145 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.440 100.509 1435 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.89 % Allowed : 22.47 % 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: -0.03 (0.24), residues: 1258 helix: 1.45 (0.32), residues: 297 sheet: -0.17 (0.41), residues: 151 loop : -0.54 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 331 HIS 0.003 0.000 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 ********************** 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 fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7815 (t160) cc_final: 0.7393 (t0) REVERT: B 84 THR cc_start: 0.8597 (m) cc_final: 0.8360 (p) REVERT: B 100 GLU cc_start: 0.8488 (tp30) cc_final: 0.8163 (tp30) REVERT: B 178 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9155 (mtt) REVERT: B 318 GLN cc_start: 0.8197 (mt0) cc_final: 0.7819 (mt0) outliers start: 19 outliers final: 17 residues processed: 85 average time/residue: 1.1702 time to fit residues: 108.4368 Evaluate side-chains 85 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 0.0020 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.2953 r_free = 0.2953 target = 0.071308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.057857 restraints weight = 19359.000| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.19 r_work: 0.2578 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 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 : 0.003 0.041 10257 Z= 0.182 Angle : 0.597 14.237 14033 Z= 0.279 Chirality : 0.044 0.145 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.395 100.558 1435 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.69 % Allowed : 22.66 % 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: -0.02 (0.24), residues: 1258 helix: 1.47 (0.32), residues: 297 sheet: -0.18 (0.41), residues: 151 loop : -0.54 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.003 0.000 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3160.20 seconds wall clock time: 56 minutes 8.64 seconds (3368.64 seconds total)