Starting phenix.real_space_refine on Thu Jul 2 05:00:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v8b_31796/07_2026/7v8b_31796.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8b_31796/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7v8b_31796/07_2026/7v8b_31796.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v8b_31796/07_2026/7v8b_31796.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v8b_31796/07_2026/7v8b_31796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8b_31796/07_2026/7v8b_31796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v8b_31796/07_2026/7v8b_31796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8b_31796/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 1.66, per 1000 atoms: 0.25 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: 0.59 Conformation dependent library (CDL) restraints added in 401.9 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: 0.15 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: 0.95 Time building geometry restraints manager: 0.76 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 - 17.94: 3486 17.94 - 35.87: 365 35.87 - 53.81: 56 53.81 - 71.74: 13 71.74 - 89.68: 7 Dihedral angle restraints: 3927 sinusoidal: 1589 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 3924 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: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.650 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 14.744 89.678 2406 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/Z covalent geometry : bond 0.00330 / 0.16 ( 6832) covalent geometry : angle 0.58633 / 0.29 ( 9282) SS BOND : bond 0.00353 / 0.18 ( 7) SS BOND : angle 2.82991 / 1.50 ( 14) hydrogen bonds : bond 0.17228 / 11.02 ( 281) hydrogen bonds : angle 5.97362 / 4.13 ( 786) link_BETA1-4 : bond 0.00569 / 0.35 ( 6) link_BETA1-4 : angle 1.59446 / 0.84 ( 18) link_NAG-ASN : bond 0.00204 / 0.07 ( 7) link_NAG-ASN : angle 2.38187 / 1.76 ( 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: 0.0763 time to fit residues: 6.3890 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 : 0.206 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.056229 restraints weight = 21716.506| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.34 r_work: 0.2846 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0895 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= 0.170 Angle : 0.601 9.589 9335 Z= 0.304 Chirality : 0.043 0.253 1010 Planarity : 0.004 0.038 1184 Dihedral : 4.411 23.363 866 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.67 % Favored : 94.20 % 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: 0.01 (0.30), residues: 793 helix: 1.01 (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 F 50 PHE 0.009 0.001 PHE F 523 TRP 0.013 0.001 TRP F 477 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 6832) covalent geometry : angle 0.58086 / 0.30 ( 9282) SS BOND : bond 0.00315 / 0.16 ( 7) SS BOND : angle 2.63548 / 1.34 ( 14) hydrogen bonds : bond 0.05230 / 3.41 ( 281) hydrogen bonds : angle 4.55586 / 3.09 ( 786) link_BETA1-4 : bond 0.00501 / 0.30 ( 6) link_BETA1-4 : angle 1.52410 / 0.83 ( 18) link_NAG-ASN : bond 0.00322 / 0.09 ( 7) link_NAG-ASN : angle 2.19675 / 1.51 ( 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 : 0.196 Fit side-chains REVERT: A 516 GLU cc_start: 0.7221 (tt0) cc_final: 0.6955 (tt0) REVERT: F 427 ASP cc_start: 0.9022 (p0) cc_final: 0.8762 (p0) outliers start: 2 outliers final: 0 residues processed: 52 average time/residue: 0.0804 time to fit residues: 5.8644 Evaluate side-chains 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 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: 3.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 4 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.068430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055309 restraints weight = 21249.193| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.30 r_work: 0.2902 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1104 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= 0.116 Angle : 0.545 9.552 9335 Z= 0.273 Chirality : 0.041 0.247 1010 Planarity : 0.003 0.034 1184 Dihedral : 4.262 23.023 866 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.92 % Favored : 94.96 % Rotamer: Outliers : 0.57 % Allowed : 10.00 % 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: 0.11 (0.31), residues: 793 helix: 1.18 (0.29), residues: 377 sheet: 1.29 (0.81), residues: 46 loop : -1.29 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 192 TYR 0.010 0.001 TYR A 489 PHE 0.008 0.001 PHE F 369 TRP 0.015 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6832) covalent geometry : angle 0.52897 / 0.27 ( 9282) SS BOND : bond 0.00189 / 0.09 ( 7) SS BOND : angle 2.14969 / 1.07 ( 14) hydrogen bonds : bond 0.04212 / 2.71 ( 281) hydrogen bonds : angle 4.23325 / 2.88 ( 786) link_BETA1-4 : bond 0.00475 / 0.29 ( 6) link_BETA1-4 : angle 1.37181 / 0.74 ( 18) link_NAG-ASN : bond 0.00222 / 0.09 ( 7) link_NAG-ASN : angle 1.93042 / 1.31 ( 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 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.215 Fit side-chains REVERT: A 386 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8793 (tptt) REVERT: A 516 GLU cc_start: 0.7184 (tt0) cc_final: 0.6943 (tt0) REVERT: F 427 ASP cc_start: 0.8935 (p0) cc_final: 0.8643 (p0) outliers start: 4 outliers final: 1 residues processed: 52 average time/residue: 0.0789 time to fit residues: 5.8092 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 : 0.170 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054391 restraints weight = 22226.845| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.36 r_work: 0.2847 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6852 Z= 0.199 Angle : 0.603 9.632 9335 Z= 0.302 Chirality : 0.043 0.256 1010 Planarity : 0.004 0.032 1184 Dihedral : 4.428 22.609 866 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.55 % Favored : 94.33 % Rotamer: Outliers : 1.57 % Allowed : 11.00 % 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: 0.08 (0.31), residues: 793 helix: 1.16 (0.29), residues: 377 sheet: 1.55 (0.84), residues: 44 loop : -1.34 (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 0.012 0.001 PHE F 523 TRP 0.014 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 6832) covalent geometry : angle 0.58335 / 0.30 ( 9282) SS BOND : bond 0.00586 / 0.21 ( 7) SS BOND : angle 2.52209 / 1.32 ( 14) hydrogen bonds : bond 0.04996 / 3.19 ( 281) hydrogen bonds : angle 4.26954 / 2.91 ( 786) link_BETA1-4 : bond 0.00419 / 0.26 ( 6) link_BETA1-4 : angle 1.46045 / 0.80 ( 18) link_NAG-ASN : bond 0.00375 / 0.10 ( 7) link_NAG-ASN : angle 2.29089 / 1.51 ( 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: 11 poor density : 46 time to evaluate : 0.223 Fit side-chains REVERT: A 386 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8780 (tptt) REVERT: A 516 GLU cc_start: 0.7426 (tt0) cc_final: 0.7150 (tt0) REVERT: F 427 ASP cc_start: 0.8944 (p0) cc_final: 0.8678 (p0) outliers start: 11 outliers final: 3 residues processed: 55 average time/residue: 0.0778 time to fit residues: 6.0533 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 : 0.215 ------------------------------------------------------------------------------- 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: 0.3980 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 0.0270 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.070614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.056441 restraints weight = 22221.037| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.39 r_work: 0.2905 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6852 Z= 0.098 Angle : 0.534 9.590 9335 Z= 0.266 Chirality : 0.040 0.251 1010 Planarity : 0.003 0.031 1184 Dihedral : 4.220 22.159 866 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 1.43 % Allowed : 12.43 % Favored : 86.14 % 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: 0.20 (0.31), residues: 793 helix: 1.33 (0.29), residues: 376 sheet: 1.31 (0.83), residues: 46 loop : -1.33 (0.31), residues: 371 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 0.010 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/Z covalent geometry : bond 0.00216 / 0.10 ( 6832) covalent geometry : angle 0.51883 / 0.26 ( 9282) SS BOND : bond 0.00227 / 0.09 ( 7) SS BOND : angle 2.12783 / 1.09 ( 14) hydrogen bonds : bond 0.03832 / 2.44 ( 281) hydrogen bonds : angle 4.07025 / 2.78 ( 786) link_BETA1-4 : bond 0.00492 / 0.30 ( 6) link_BETA1-4 : angle 1.29626 / 0.71 ( 18) link_NAG-ASN : bond 0.00204 / 0.11 ( 7) link_NAG-ASN : angle 1.80518 / 1.22 ( 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 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.8501 (m-30) cc_final: 0.7981 (m-30) REVERT: A 516 GLU cc_start: 0.7302 (tt0) cc_final: 0.7095 (tt0) REVERT: F 95 LEU cc_start: 0.9553 (tt) cc_final: 0.9317 (tt) REVERT: F 427 ASP cc_start: 0.8986 (p0) cc_final: 0.8676 (p0) REVERT: F 479 GLU cc_start: 0.8281 (pt0) cc_final: 0.7993 (pt0) outliers start: 10 outliers final: 3 residues processed: 60 average time/residue: 0.0666 time to fit residues: 5.6422 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.070458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.056294 restraints weight = 22143.786| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.39 r_work: 0.2902 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6852 Z= 0.107 Angle : 0.546 9.640 9335 Z= 0.269 Chirality : 0.041 0.256 1010 Planarity : 0.003 0.030 1184 Dihedral : 4.147 21.065 866 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 1.57 % Allowed : 13.14 % 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: 0.29 (0.31), residues: 793 helix: 1.40 (0.29), residues: 375 sheet: 1.32 (0.84), residues: 46 loop : -1.26 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.011 0.001 TYR F 183 PHE 0.009 0.001 PHE F 523 TRP 0.012 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6832) covalent geometry : angle 0.53195 / 0.27 ( 9282) SS BOND : bond 0.00222 / 0.10 ( 7) SS BOND : angle 2.02853 / 1.05 ( 14) hydrogen bonds : bond 0.03850 / 2.47 ( 281) hydrogen bonds : angle 4.02423 / 2.76 ( 786) link_BETA1-4 : bond 0.00460 / 0.28 ( 6) link_BETA1-4 : angle 1.29078 / 0.71 ( 18) link_NAG-ASN : bond 0.00187 / 0.08 ( 7) link_NAG-ASN : angle 1.79355 / 1.20 ( 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 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.258 Fit side-chains REVERT: A 442 ASP cc_start: 0.8619 (m-30) cc_final: 0.8108 (m-30) REVERT: F 95 LEU cc_start: 0.9541 (tt) cc_final: 0.9295 (tt) REVERT: F 427 ASP cc_start: 0.8969 (p0) cc_final: 0.8657 (p0) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.0730 time to fit residues: 6.3053 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 259 ILE Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 26 optimal weight: 0.0000 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.054521 restraints weight = 21921.942| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.36 r_work: 0.2855 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6852 Z= 0.191 Angle : 0.611 9.735 9335 Z= 0.303 Chirality : 0.043 0.261 1010 Planarity : 0.003 0.029 1184 Dihedral : 4.358 21.545 866 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.55 % Favored : 94.33 % Rotamer: Outliers : 1.29 % Allowed : 13.71 % 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: 0.26 (0.31), residues: 793 helix: 1.37 (0.29), residues: 375 sheet: 1.56 (0.85), residues: 44 loop : -1.30 (0.32), residues: 374 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 0.014 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 6832) covalent geometry : angle 0.59276 / 0.30 ( 9282) SS BOND : bond 0.00467 / 0.22 ( 7) SS BOND : angle 2.53890 / 1.33 ( 14) hydrogen bonds : bond 0.04782 / 3.06 ( 281) hydrogen bonds : angle 4.14430 / 2.83 ( 786) link_BETA1-4 : bond 0.00461 / 0.28 ( 6) link_BETA1-4 : angle 1.38288 / 0.75 ( 18) link_NAG-ASN : bond 0.00336 / 0.08 ( 7) link_NAG-ASN : angle 2.16513 / 1.43 ( 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 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.215 Fit side-chains REVERT: A 442 ASP cc_start: 0.8686 (m-30) cc_final: 0.8454 (m-30) REVERT: F 95 LEU cc_start: 0.9565 (tt) cc_final: 0.9319 (tt) REVERT: F 427 ASP cc_start: 0.9006 (p0) cc_final: 0.8718 (p0) outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 0.0696 time to fit residues: 5.3727 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 : 0.192 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 491 VAL 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: 2.9990 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 0.0570 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.070162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.055992 restraints weight = 21953.744| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.39 r_work: 0.2893 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6852 Z= 0.109 Angle : 0.571 9.646 9335 Z= 0.281 Chirality : 0.041 0.254 1010 Planarity : 0.003 0.028 1184 Dihedral : 4.234 20.905 866 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 1.14 % Allowed : 14.29 % 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: 0.32 (0.31), residues: 793 helix: 1.43 (0.29), residues: 375 sheet: 1.52 (0.85), residues: 44 loop : -1.27 (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 0.008 0.001 PHE F 603 TRP 0.014 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6832) covalent geometry : angle 0.55743 / 0.28 ( 9282) SS BOND : bond 0.00236 / 0.11 ( 7) SS BOND : angle 2.08276 / 1.07 ( 14) hydrogen bonds : bond 0.03885 / 2.47 ( 281) hydrogen bonds : angle 4.02089 / 2.75 ( 786) link_BETA1-4 : bond 0.00515 / 0.31 ( 6) link_BETA1-4 : angle 1.27724 / 0.70 ( 18) link_NAG-ASN : bond 0.00183 / 0.09 ( 7) link_NAG-ASN : angle 1.79542 / 1.21 ( 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.155 Fit side-chains REVERT: A 420 ASP cc_start: 0.8840 (m-30) cc_final: 0.8592 (m-30) REVERT: A 442 ASP cc_start: 0.8638 (m-30) cc_final: 0.8111 (m-30) REVERT: A 516 GLU cc_start: 0.6988 (tt0) cc_final: 0.6762 (tt0) REVERT: F 95 LEU cc_start: 0.9554 (tt) cc_final: 0.9309 (tt) REVERT: F 427 ASP cc_start: 0.8973 (p0) cc_final: 0.8674 (p0) REVERT: F 479 GLU cc_start: 0.8208 (pt0) cc_final: 0.7891 (pt0) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.0626 time to fit residues: 5.0029 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 : 0.248 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054986 restraints weight = 22142.717| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.39 r_work: 0.2869 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6852 Z= 0.152 Angle : 0.590 9.696 9335 Z= 0.294 Chirality : 0.042 0.259 1010 Planarity : 0.003 0.029 1184 Dihedral : 4.272 20.546 866 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.67 % Favored : 94.20 % Rotamer: Outliers : 1.00 % Allowed : 14.29 % Favored : 84.71 % 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: 0.28 (0.31), residues: 793 helix: 1.43 (0.29), residues: 375 sheet: 1.30 (0.84), residues: 46 loop : -1.32 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 482 TYR 0.013 0.001 TYR F 183 PHE 0.011 0.001 PHE F 523 TRP 0.014 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6832) covalent geometry : angle 0.57441 / 0.29 ( 9282) SS BOND : bond 0.00297 / 0.14 ( 7) SS BOND : angle 2.36359 / 1.21 ( 14) hydrogen bonds : bond 0.04379 / 2.79 ( 281) hydrogen bonds : angle 4.06674 / 2.78 ( 786) link_BETA1-4 : bond 0.00470 / 0.29 ( 6) link_BETA1-4 : angle 1.31653 / 0.72 ( 18) link_NAG-ASN : bond 0.00260 / 0.07 ( 7) link_NAG-ASN : angle 1.97717 / 1.31 ( 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: 7 poor density : 47 time to evaluate : 0.211 Fit side-chains REVERT: A 442 ASP cc_start: 0.8672 (m-30) cc_final: 0.8125 (m-30) REVERT: F 95 LEU cc_start: 0.9568 (tt) cc_final: 0.9318 (tt) REVERT: F 427 ASP cc_start: 0.8930 (p0) cc_final: 0.8651 (p0) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.0747 time to fit residues: 5.7192 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 F residue 160 GLU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.070252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056086 restraints weight = 21831.080| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.37 r_work: 0.2899 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6852 Z= 0.111 Angle : 0.574 10.434 9335 Z= 0.284 Chirality : 0.041 0.253 1010 Planarity : 0.003 0.029 1184 Dihedral : 4.179 21.437 866 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 1.00 % Allowed : 14.71 % Favored : 84.29 % 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: 0.34 (0.31), residues: 793 helix: 1.52 (0.29), residues: 369 sheet: 1.31 (0.84), residues: 46 loop : -1.28 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 403 TYR 0.012 0.001 TYR F 183 PHE 0.008 0.001 PHE F 603 TRP 0.012 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6832) covalent geometry : angle 0.56138 / 0.28 ( 9282) SS BOND : bond 0.00213 / 0.10 ( 7) SS BOND : angle 2.08250 / 1.05 ( 14) hydrogen bonds : bond 0.03797 / 2.41 ( 281) hydrogen bonds : angle 3.99775 / 2.74 ( 786) link_BETA1-4 : bond 0.00484 / 0.29 ( 6) link_BETA1-4 : angle 1.26719 / 0.69 ( 18) link_NAG-ASN : bond 0.00182 / 0.08 ( 7) link_NAG-ASN : angle 1.75090 / 1.18 ( 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.220 Fit side-chains REVERT: A 420 ASP cc_start: 0.8858 (m-30) cc_final: 0.8502 (m-30) REVERT: A 442 ASP cc_start: 0.8626 (m-30) cc_final: 0.8080 (m-30) REVERT: F 95 LEU cc_start: 0.9553 (tt) cc_final: 0.9304 (tt) REVERT: F 190 MET cc_start: 0.8781 (tmm) cc_final: 0.8571 (tmm) REVERT: F 250 ASN cc_start: 0.7646 (m-40) cc_final: 0.7346 (m-40) REVERT: F 376 MET cc_start: 0.9369 (tpp) cc_final: 0.9013 (mmt) REVERT: F 427 ASP cc_start: 0.8977 (p0) cc_final: 0.8690 (p0) outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 0.0672 time to fit residues: 5.5524 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 : 0.230 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.068767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054606 restraints weight = 21810.499| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.36 r_work: 0.2860 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6852 Z= 0.169 Angle : 0.608 10.240 9335 Z= 0.302 Chirality : 0.043 0.260 1010 Planarity : 0.003 0.028 1184 Dihedral : 4.328 21.617 866 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.67 % Favored : 94.20 % Rotamer: Outliers : 0.86 % Allowed : 14.86 % Favored : 84.29 % 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: 0.32 (0.31), residues: 793 helix: 1.49 (0.29), residues: 369 sheet: 1.56 (0.85), residues: 44 loop : -1.30 (0.31), residues: 380 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 0.012 0.001 PHE F 523 TRP 0.017 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 6832) covalent geometry : angle 0.59171 / 0.30 ( 9282) SS BOND : bond 0.00322 / 0.15 ( 7) SS BOND : angle 2.40041 / 1.27 ( 14) hydrogen bonds : bond 0.04593 / 2.93 ( 281) hydrogen bonds : angle 4.08844 / 2.80 ( 786) link_BETA1-4 : bond 0.00486 / 0.30 ( 6) link_BETA1-4 : angle 1.36013 / 0.75 ( 18) link_NAG-ASN : bond 0.00296 / 0.07 ( 7) link_NAG-ASN : angle 2.06020 / 1.36 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.72 seconds wall clock time: 29 minutes 8.65 seconds (1748.65 seconds total)