Starting phenix.real_space_refine on Tue Mar 3 15:54:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v8b_31796/03_2026/7v8b_31796.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8b_31796/03_2026/7v8b_31796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v8b_31796/03_2026/7v8b_31796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8b_31796/03_2026/7v8b_31796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v8b_31796/03_2026/7v8b_31796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8b_31796/03_2026/7v8b_31796.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4242 2.51 5 N 1088 2.21 5 O 1283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6650 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.50, per 1000 atoms: 0.23 Number of scatterers: 6650 At special positions: 0 Unit cell: (79.2, 105.6, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1283 8.00 N 1088 7.00 C 4242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.02 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN F 90 " " NAG D 1 " - " ASN F 103 " " NAG E 1 " - " ASN F 322 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 432 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 177.5 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 55.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.667A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.835A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.987A pdb=" N TYR A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.797A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 58 Processing helix chain 'F' and resid 59 through 80 removed outlier: 4.515A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.765A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.877A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.812A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 157 through 172 Processing helix chain 'F' and resid 175 through 194 removed outlier: 4.361A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.513A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 231 removed outlier: 3.890A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.635A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.182A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.532A pdb=" N GLU F 312 " --> pdb=" O PHE F 308 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.956A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.645A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.509A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.757A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 485 removed outlier: 3.790A pdb=" N TRP F 478 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 482 " --> pdb=" O TRP F 478 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.560A pdb=" N THR F 517 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.785A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 564 removed outlier: 4.468A pdb=" N GLU F 564 " --> pdb=" O GLY F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.950A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'F' and resid 347 through 350 281 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2109 1.34 - 1.46: 1732 1.46 - 1.58: 2933 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6832 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" C1 NAG F2001 " pdb=" O5 NAG F2001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 ... (remaining 6827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 9056 1.66 - 3.31: 194 3.31 - 4.97: 23 4.97 - 6.63: 6 6.63 - 8.28: 3 Bond angle restraints: 9282 Sorted by residual: angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 122.68 -8.28 2.30e+00 1.89e-01 1.30e+01 angle pdb=" CB ARG F 192 " pdb=" CG ARG F 192 " pdb=" CD ARG F 192 " ideal model delta sigma weight residual 111.30 118.38 -7.08 2.30e+00 1.89e-01 9.49e+00 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 120.75 -6.35 2.30e+00 1.89e-01 7.62e+00 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 108.79 112.66 -3.87 1.53e+00 4.27e-01 6.40e+00 angle pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 116.30 124.32 -8.02 3.50e+00 8.16e-02 5.25e+00 ... (remaining 9277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 3857 21.70 - 43.40: 304 43.40 - 65.10: 36 65.10 - 86.80: 15 86.80 - 108.49: 7 Dihedral angle restraints: 4219 sinusoidal: 1881 harmonic: 2338 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 3.62 89.38 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ASN F 432 " pdb=" C ASN F 432 " pdb=" N GLU F 433 " pdb=" CA GLU F 433 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 4216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 825 0.055 - 0.110: 164 0.110 - 0.164: 18 0.164 - 0.219: 2 0.219 - 0.274: 1 Chirality restraints: 1010 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA CYS A 391 " pdb=" N CYS A 391 " pdb=" C CYS A 391 " pdb=" CB CYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 1007 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 192 " -0.129 9.50e-02 1.11e+02 5.82e-02 2.64e+00 pdb=" NE ARG F 192 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 192 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG F 192 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 192 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 425 " -0.025 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO F 426 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 426 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 426 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 134 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO F 135 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 135 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 135 " -0.021 5.00e-02 4.00e+02 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2068 2.83 - 3.34: 6211 3.34 - 3.86: 10347 3.86 - 4.38: 11645 4.38 - 4.90: 20266 Nonbonded interactions: 50537 Sorted by model distance: nonbonded pdb=" OG SER A 349 " pdb=" O ARG A 452 " model vdw 2.308 3.040 nonbonded pdb=" O THR F 125 " pdb=" OG1 THR F 129 " model vdw 2.311 3.040 nonbonded pdb=" NH1 ARG F 177 " pdb=" O GLU F 495 " model vdw 2.340 3.120 nonbonded pdb=" NH1 ARG F 161 " pdb=" O HIS F 265 " model vdw 2.357 3.120 nonbonded pdb=" NE1 TRP F 271 " pdb=" O SER F 502 " model vdw 2.380 3.120 ... (remaining 50532 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } 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: 4.450 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.003 0.036 6852 Z= 0.159 Angle : 0.610 8.282 9335 Z= 0.297 Chirality : 0.044 0.274 1010 Planarity : 0.004 0.058 1184 Dihedral : 15.613 108.494 2698 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.30), residues: 793 helix: 0.72 (0.28), residues: 369 sheet: 1.04 (0.80), residues: 47 loop : -1.38 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 192 TYR 0.012 0.001 TYR F 50 PHE 0.011 0.001 PHE F 603 TRP 0.015 0.001 TRP F 477 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6832) covalent geometry : angle 0.58633 ( 9282) SS BOND : bond 0.00353 ( 7) SS BOND : angle 2.82991 ( 14) hydrogen bonds : bond 0.17228 ( 281) hydrogen bonds : angle 5.97362 ( 786) link_BETA1-4 : bond 0.00569 ( 6) link_BETA1-4 : angle 1.59446 ( 18) link_NAG-ASN : bond 0.00204 ( 7) link_NAG-ASN : angle 2.38187 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.247 Fit side-chains REVERT: A 516 GLU cc_start: 0.6126 (tt0) cc_final: 0.5917 (tt0) REVERT: F 427 ASP cc_start: 0.7731 (p0) cc_final: 0.7337 (p0) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0722 time to fit residues: 5.9838 Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.056214 restraints weight = 21725.806| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.33 r_work: 0.2846 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6852 Z= 0.171 Angle : 0.611 9.615 9335 Z= 0.306 Chirality : 0.043 0.243 1010 Planarity : 0.004 0.037 1184 Dihedral : 8.573 61.456 1158 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.80 % Favored : 94.07 % Rotamer: Outliers : 0.29 % Allowed : 7.43 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.30), residues: 793 helix: 1.00 (0.28), residues: 370 sheet: 1.46 (0.82), residues: 44 loop : -1.21 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 192 TYR 0.012 0.001 TYR A 369 PHE 0.009 0.001 PHE F 523 TRP 0.014 0.001 TRP F 477 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6832) covalent geometry : angle 0.58857 ( 9282) SS BOND : bond 0.00327 ( 7) SS BOND : angle 2.63905 ( 14) hydrogen bonds : bond 0.05224 ( 281) hydrogen bonds : angle 4.55579 ( 786) link_BETA1-4 : bond 0.00405 ( 6) link_BETA1-4 : angle 1.87880 ( 18) link_NAG-ASN : bond 0.00337 ( 7) link_NAG-ASN : angle 2.22542 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.269 Fit side-chains REVERT: A 516 GLU cc_start: 0.7230 (tt0) cc_final: 0.6968 (tt0) REVERT: F 376 MET cc_start: 0.9465 (tpp) cc_final: 0.9263 (mmt) REVERT: F 427 ASP cc_start: 0.9024 (p0) cc_final: 0.8761 (p0) outliers start: 2 outliers final: 0 residues processed: 52 average time/residue: 0.0825 time to fit residues: 6.0420 Evaluate side-chains 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.070278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.056120 restraints weight = 21901.390| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.38 r_work: 0.2894 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6852 Z= 0.123 Angle : 0.556 9.602 9335 Z= 0.277 Chirality : 0.042 0.241 1010 Planarity : 0.003 0.034 1184 Dihedral : 6.997 55.945 1158 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.92 % Favored : 94.96 % Rotamer: Outliers : 0.71 % Allowed : 9.86 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.31), residues: 793 helix: 1.17 (0.29), residues: 377 sheet: 1.28 (0.81), residues: 46 loop : -1.30 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 192 TYR 0.011 0.001 TYR F 50 PHE 0.008 0.001 PHE F 369 TRP 0.014 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6832) covalent geometry : angle 0.53789 ( 9282) SS BOND : bond 0.00241 ( 7) SS BOND : angle 2.18855 ( 14) hydrogen bonds : bond 0.04320 ( 281) hydrogen bonds : angle 4.24434 ( 786) link_BETA1-4 : bond 0.00461 ( 6) link_BETA1-4 : angle 1.72864 ( 18) link_NAG-ASN : bond 0.00252 ( 7) link_NAG-ASN : angle 1.98768 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.253 Fit side-chains REVERT: A 386 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8787 (tptt) REVERT: A 516 GLU cc_start: 0.7200 (tt0) cc_final: 0.6944 (tt0) REVERT: F 427 ASP cc_start: 0.8936 (p0) cc_final: 0.8648 (p0) outliers start: 5 outliers final: 1 residues processed: 53 average time/residue: 0.0813 time to fit residues: 6.0809 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055147 restraints weight = 22155.240| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.39 r_work: 0.2863 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6852 Z= 0.163 Angle : 0.572 9.697 9335 Z= 0.285 Chirality : 0.042 0.244 1010 Planarity : 0.003 0.032 1184 Dihedral : 6.514 55.918 1158 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.42 % Favored : 94.45 % Rotamer: Outliers : 1.43 % Allowed : 11.14 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.31), residues: 793 helix: 1.18 (0.29), residues: 377 sheet: 1.54 (0.83), residues: 44 loop : -1.30 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 460 TYR 0.012 0.001 TYR F 183 PHE 0.011 0.001 PHE F 523 TRP 0.014 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6832) covalent geometry : angle 0.55203 ( 9282) SS BOND : bond 0.00325 ( 7) SS BOND : angle 2.37894 ( 14) hydrogen bonds : bond 0.04593 ( 281) hydrogen bonds : angle 4.20812 ( 786) link_BETA1-4 : bond 0.00376 ( 6) link_BETA1-4 : angle 1.60667 ( 18) link_NAG-ASN : bond 0.00303 ( 7) link_NAG-ASN : angle 2.14168 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.265 Fit side-chains REVERT: A 386 LYS cc_start: 0.9051 (tmtt) cc_final: 0.8775 (tptt) REVERT: A 442 ASP cc_start: 0.8545 (m-30) cc_final: 0.8021 (m-30) REVERT: A 516 GLU cc_start: 0.7366 (tt0) cc_final: 0.7071 (tt0) REVERT: F 427 ASP cc_start: 0.8946 (p0) cc_final: 0.8683 (p0) outliers start: 10 outliers final: 3 residues processed: 55 average time/residue: 0.0715 time to fit residues: 5.5692 Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052990 restraints weight = 21772.041| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.32 r_work: 0.2860 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6852 Z= 0.203 Angle : 0.603 9.780 9335 Z= 0.303 Chirality : 0.043 0.253 1010 Planarity : 0.004 0.030 1184 Dihedral : 6.566 55.278 1158 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 1.86 % Allowed : 12.14 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.31), residues: 793 helix: 1.23 (0.28), residues: 376 sheet: 1.55 (0.84), residues: 44 loop : -1.40 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.013 0.001 TYR F 183 PHE 0.013 0.001 PHE F 523 TRP 0.017 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 6832) covalent geometry : angle 0.58257 ( 9282) SS BOND : bond 0.00397 ( 7) SS BOND : angle 2.62956 ( 14) hydrogen bonds : bond 0.04980 ( 281) hydrogen bonds : angle 4.25344 ( 786) link_BETA1-4 : bond 0.00438 ( 6) link_BETA1-4 : angle 1.51507 ( 18) link_NAG-ASN : bond 0.00381 ( 7) link_NAG-ASN : angle 2.29199 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.265 Fit side-chains REVERT: A 516 GLU cc_start: 0.7451 (tt0) cc_final: 0.7205 (tt0) REVERT: F 427 ASP cc_start: 0.8964 (p0) cc_final: 0.8672 (p0) outliers start: 13 outliers final: 4 residues processed: 56 average time/residue: 0.0714 time to fit residues: 5.6494 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055425 restraints weight = 22179.885| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.38 r_work: 0.2873 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6852 Z= 0.115 Angle : 0.557 9.720 9335 Z= 0.278 Chirality : 0.041 0.245 1010 Planarity : 0.003 0.029 1184 Dihedral : 6.330 55.514 1158 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 1.43 % Allowed : 13.29 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.31), residues: 793 helix: 1.31 (0.29), residues: 375 sheet: 1.52 (0.84), residues: 44 loop : -1.32 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 460 TYR 0.012 0.001 TYR F 183 PHE 0.010 0.001 PHE F 603 TRP 0.014 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6832) covalent geometry : angle 0.54118 ( 9282) SS BOND : bond 0.00251 ( 7) SS BOND : angle 2.11849 ( 14) hydrogen bonds : bond 0.04117 ( 281) hydrogen bonds : angle 4.11592 ( 786) link_BETA1-4 : bond 0.00435 ( 6) link_BETA1-4 : angle 1.39722 ( 18) link_NAG-ASN : bond 0.00214 ( 7) link_NAG-ASN : angle 1.94925 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.226 Fit side-chains REVERT: F 95 LEU cc_start: 0.9556 (tt) cc_final: 0.9314 (tt) REVERT: F 376 MET cc_start: 0.9439 (tpp) cc_final: 0.9175 (tpp) REVERT: F 427 ASP cc_start: 0.8978 (p0) cc_final: 0.8687 (p0) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.0774 time to fit residues: 6.3639 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 401 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 26 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.0870 chunk 40 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.069521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.055326 restraints weight = 21910.918| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.38 r_work: 0.2871 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6852 Z= 0.135 Angle : 0.575 9.768 9335 Z= 0.283 Chirality : 0.041 0.248 1010 Planarity : 0.003 0.029 1184 Dihedral : 6.260 55.355 1158 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 1.57 % Allowed : 13.43 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.31), residues: 793 helix: 1.34 (0.29), residues: 375 sheet: 1.51 (0.85), residues: 44 loop : -1.30 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.012 0.001 TYR F 183 PHE 0.011 0.001 PHE F 523 TRP 0.014 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6832) covalent geometry : angle 0.55815 ( 9282) SS BOND : bond 0.00281 ( 7) SS BOND : angle 2.31479 ( 14) hydrogen bonds : bond 0.04274 ( 281) hydrogen bonds : angle 4.09012 ( 786) link_BETA1-4 : bond 0.00429 ( 6) link_BETA1-4 : angle 1.37442 ( 18) link_NAG-ASN : bond 0.00246 ( 7) link_NAG-ASN : angle 2.01724 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.265 Fit side-chains REVERT: F 95 LEU cc_start: 0.9563 (tt) cc_final: 0.9315 (tt) REVERT: F 376 MET cc_start: 0.9490 (tpp) cc_final: 0.9254 (mmt) REVERT: F 427 ASP cc_start: 0.8925 (p0) cc_final: 0.8640 (p0) REVERT: F 479 GLU cc_start: 0.8247 (pt0) cc_final: 0.7981 (pt0) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.0804 time to fit residues: 6.3872 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 401 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 39 optimal weight: 0.3980 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 0.0060 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 overall best weight: 0.2812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057208 restraints weight = 21938.435| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.40 r_work: 0.2922 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6852 Z= 0.096 Angle : 0.558 10.099 9335 Z= 0.275 Chirality : 0.040 0.240 1010 Planarity : 0.003 0.028 1184 Dihedral : 5.968 55.423 1158 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 0.71 % Allowed : 14.71 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.31), residues: 793 helix: 1.41 (0.29), residues: 375 sheet: 1.47 (0.84), residues: 44 loop : -1.22 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 460 TYR 0.011 0.001 TYR F 183 PHE 0.009 0.001 PHE F 327 TRP 0.015 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 6832) covalent geometry : angle 0.54584 ( 9282) SS BOND : bond 0.00169 ( 7) SS BOND : angle 1.85789 ( 14) hydrogen bonds : bond 0.03331 ( 281) hydrogen bonds : angle 3.94937 ( 786) link_BETA1-4 : bond 0.00473 ( 6) link_BETA1-4 : angle 1.32286 ( 18) link_NAG-ASN : bond 0.00203 ( 7) link_NAG-ASN : angle 1.65739 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.231 Fit side-chains REVERT: A 420 ASP cc_start: 0.8823 (m-30) cc_final: 0.8561 (m-30) REVERT: F 95 LEU cc_start: 0.9533 (tt) cc_final: 0.9281 (tt) REVERT: F 250 ASN cc_start: 0.7638 (m-40) cc_final: 0.7357 (m-40) REVERT: F 427 ASP cc_start: 0.8970 (p0) cc_final: 0.8666 (p0) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.0787 time to fit residues: 6.5361 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 401 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054929 restraints weight = 22217.453| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.39 r_work: 0.2863 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6852 Z= 0.167 Angle : 0.626 12.499 9335 Z= 0.304 Chirality : 0.042 0.249 1010 Planarity : 0.003 0.029 1184 Dihedral : 6.152 55.475 1158 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.80 % Favored : 94.07 % Rotamer: Outliers : 0.86 % Allowed : 15.00 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.31), residues: 793 helix: 1.43 (0.29), residues: 375 sheet: 1.31 (0.84), residues: 46 loop : -1.28 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.013 0.001 TYR F 183 PHE 0.012 0.001 PHE F 523 TRP 0.010 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 6832) covalent geometry : angle 0.61011 ( 9282) SS BOND : bond 0.00323 ( 7) SS BOND : angle 2.43037 ( 14) hydrogen bonds : bond 0.04440 ( 281) hydrogen bonds : angle 4.04620 ( 786) link_BETA1-4 : bond 0.00449 ( 6) link_BETA1-4 : angle 1.36748 ( 18) link_NAG-ASN : bond 0.00302 ( 7) link_NAG-ASN : angle 2.06530 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.275 Fit side-chains REVERT: A 516 GLU cc_start: 0.7130 (tt0) cc_final: 0.6919 (tt0) REVERT: F 95 LEU cc_start: 0.9562 (tt) cc_final: 0.9302 (tt) REVERT: F 427 ASP cc_start: 0.8948 (p0) cc_final: 0.8717 (p0) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.0782 time to fit residues: 5.9566 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 401 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 0.0470 chunk 57 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.070138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055972 restraints weight = 21876.635| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.36 r_work: 0.2891 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6852 Z= 0.110 Angle : 0.604 13.206 9335 Z= 0.291 Chirality : 0.041 0.242 1010 Planarity : 0.003 0.029 1184 Dihedral : 6.121 55.614 1158 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 0.86 % Allowed : 15.43 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.31), residues: 793 helix: 1.43 (0.29), residues: 375 sheet: 1.31 (0.84), residues: 46 loop : -1.22 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.012 0.001 TYR F 183 PHE 0.009 0.001 PHE F 603 TRP 0.017 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6832) covalent geometry : angle 0.59091 ( 9282) SS BOND : bond 0.00221 ( 7) SS BOND : angle 2.14338 ( 14) hydrogen bonds : bond 0.03895 ( 281) hydrogen bonds : angle 3.97993 ( 786) link_BETA1-4 : bond 0.00445 ( 6) link_BETA1-4 : angle 1.31113 ( 18) link_NAG-ASN : bond 0.00190 ( 7) link_NAG-ASN : angle 1.80954 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.264 Fit side-chains REVERT: A 420 ASP cc_start: 0.8837 (m-30) cc_final: 0.8469 (m-30) REVERT: A 516 GLU cc_start: 0.7188 (tt0) cc_final: 0.6982 (tt0) REVERT: F 95 LEU cc_start: 0.9553 (tt) cc_final: 0.9297 (tt) REVERT: F 376 MET cc_start: 0.9353 (tpp) cc_final: 0.8992 (mmt) REVERT: F 427 ASP cc_start: 0.8967 (p0) cc_final: 0.8673 (p0) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.0754 time to fit residues: 5.7144 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 401 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.055278 restraints weight = 21810.063| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.33 r_work: 0.2871 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6852 Z= 0.147 Angle : 0.614 12.287 9335 Z= 0.297 Chirality : 0.042 0.246 1010 Planarity : 0.003 0.029 1184 Dihedral : 6.291 55.599 1158 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.67 % Favored : 94.20 % Rotamer: Outliers : 1.00 % Allowed : 15.29 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.31), residues: 793 helix: 1.41 (0.29), residues: 375 sheet: 1.32 (0.84), residues: 46 loop : -1.28 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.015 0.001 TYR F 50 PHE 0.011 0.001 PHE F 523 TRP 0.013 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6832) covalent geometry : angle 0.59816 ( 9282) SS BOND : bond 0.00356 ( 7) SS BOND : angle 2.38659 ( 14) hydrogen bonds : bond 0.04297 ( 281) hydrogen bonds : angle 4.03320 ( 786) link_BETA1-4 : bond 0.00448 ( 6) link_BETA1-4 : angle 1.33994 ( 18) link_NAG-ASN : bond 0.00257 ( 7) link_NAG-ASN : angle 1.98548 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.68 seconds wall clock time: 29 minutes 55.45 seconds (1795.45 seconds total)