Starting phenix.real_space_refine on Thu Jul 2 04:26:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v80_31785/07_2026/7v80_31785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v80_31785/07_2026/7v80_31785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v80_31785/07_2026/7v80_31785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v80_31785/07_2026/7v80_31785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v80_31785/07_2026/7v80_31785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v80_31785/07_2026/7v80_31785.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v80_31785/07_2026/7v80_31785.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v80_31785/07_2026/7v80_31785.cif" } resolution = 3.9 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= 0.037 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 4222 2.51 5 N 1082 2.21 5 O 1268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 6609 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 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: 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: "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: "A" 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.36, per 1000 atoms: 0.21 Number of scatterers: 6609 At special positions: 0 Unit cell: (74.8, 99, 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 1268 8.00 N 1082 7.00 C 4222 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B 1 " - " ASN F 90 " " NAG C 1 " - " ASN F 103 " " NAG D 1 " - " ASN F 546 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 322 " " NAG F2003 " - " ASN F 432 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 340.1 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: 35 helices and 5 sheets defined 49.2% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.760A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.651A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.662A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.720A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 53 removed outlier: 3.714A pdb=" N ALA F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 73 removed outlier: 3.598A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.583A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 152 removed outlier: 3.802A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.636A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 removed outlier: 3.528A pdb=" N TRP F 203 " --> pdb=" O TYR F 199 " (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 218 through 229 removed outlier: 3.848A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.734A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.927A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.990A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.556A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.730A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.920A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.715A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA F 413 " --> pdb=" O SER F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.519A pdb=" N GLN F 442 " --> pdb=" O PHE F 438 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 476 through 485 removed outlier: 4.969A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.117A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.836A pdb=" N ARG F 518 " --> pdb=" O ARG F 514 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.883A pdb=" N GLN F 552 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 583 through 588 removed outlier: 3.990A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 596 removed outlier: 3.703A pdb=" N PHE F 592 " --> pdb=" O PHE F 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.712A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) 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 removed outlier: 3.697A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 262 through 263 removed outlier: 7.017A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 347 through 352 removed outlier: 5.967A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 687 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: 0.88 Time building geometry restraints manager: 0.77 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: 2100 1.34 - 1.46: 1745 1.46 - 1.58: 2888 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6792 Sorted by residual: bond pdb=" CA ASP F 350 " pdb=" CB ASP F 350 " ideal model delta sigma weight residual 1.531 1.666 -0.135 3.28e-02 9.30e+02 1.69e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb=" C1 NAG F2003 " pdb=" O5 NAG F2003 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.86e+00 bond pdb=" CB PRO F 284 " pdb=" CG PRO F 284 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.44e+00 ... (remaining 6787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9084 2.19 - 4.38: 118 4.38 - 6.57: 25 6.57 - 8.76: 3 8.76 - 10.95: 1 Bond angle restraints: 9231 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 125.35 -10.95 2.30e+00 1.89e-01 2.27e+01 angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 107.88 113.57 -5.69 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N GLU F 406 " pdb=" CA GLU F 406 " pdb=" CB GLU F 406 " ideal model delta sigma weight residual 110.41 116.02 -5.61 1.68e+00 3.54e-01 1.11e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 121.52 -7.12 2.30e+00 1.89e-01 9.58e+00 angle pdb=" C ASP F 431 " pdb=" N ASN F 432 " pdb=" CA ASN F 432 " ideal model delta sigma weight residual 121.19 125.95 -4.76 1.59e+00 3.96e-01 8.95e+00 ... (remaining 9226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3473 18.00 - 36.00: 367 36.00 - 53.99: 64 53.99 - 71.99: 7 71.99 - 89.99: 10 Dihedral angle restraints: 3921 sinusoidal: 1582 harmonic: 2339 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -3.11 -82.89 1 1.00e+01 1.00e-02 8.41e+01 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 -86.00 -9.77 -76.23 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 3918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 952 0.096 - 0.191: 44 0.191 - 0.287: 1 0.287 - 0.382: 0 0.382 - 0.478: 1 Chirality restraints: 998 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN F 546 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 995 not shown) Planarity restraints: 1189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 283 " -0.039 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO F 284 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 284 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 284 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 262 " 0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO F 263 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 263 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 263 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 524 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C GLN F 524 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN F 524 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE F 525 " -0.010 2.00e-02 2.50e+03 ... (remaining 1186 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 114 2.68 - 3.23: 6334 3.23 - 3.79: 9855 3.79 - 4.34: 12459 4.34 - 4.90: 20618 Nonbonded interactions: 49380 Sorted by model distance: nonbonded pdb=" OG SER F 109 " pdb=" OD1 ASP F 111 " model vdw 2.120 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.168 3.040 nonbonded pdb=" O ILE F 151 " pdb=" OG SER F 155 " model vdw 2.188 3.040 nonbonded pdb=" OD1 ASN A 487 " pdb=" OH TYR F 83 " model vdw 2.239 3.040 nonbonded pdb=" O SER A 530 " pdb=" OG SER A 530 " model vdw 2.241 3.040 ... (remaining 49375 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 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 4.090 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.004 0.135 6810 Z= 0.171 Angle : 0.684 10.952 9278 Z= 0.346 Chirality : 0.046 0.478 998 Planarity : 0.005 0.058 1181 Dihedral : 14.996 89.988 2400 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % 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: -0.76 (0.31), residues: 793 helix: 0.30 (0.30), residues: 344 sheet: -0.70 (0.66), residues: 59 loop : -1.18 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.010 0.001 TYR A 453 PHE 0.009 0.001 PHE F 369 TRP 0.024 0.001 TRP F 478 HIS 0.004 0.001 HIS F 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 6792) covalent geometry : angle 0.64630 / 0.33 ( 9231) SS BOND : bond 0.00285 / 0.16 ( 7) SS BOND : angle 4.06508 / 2.76 ( 14) hydrogen bonds : bond 0.16892 / 11.19 ( 240) hydrogen bonds : angle 5.92475 / 4.14 ( 687) link_BETA1-4 : bond 0.00435 / 0.31 ( 3) link_BETA1-4 : angle 1.63141 / 1.16 ( 9) link_NAG-ASN : bond 0.00532 / 0.18 ( 8) link_NAG-ASN : angle 3.07901 / 2.35 ( 24) *********************** 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 96 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.245 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0734 time to fit residues: 9.9016 Evaluate side-chains 79 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.0050 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 81 GLN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122810 restraints weight = 13420.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124397 restraints weight = 9977.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125630 restraints weight = 6951.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126641 restraints weight = 5268.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126876 restraints weight = 4609.716| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6810 Z= 0.136 Angle : 0.647 10.334 9278 Z= 0.324 Chirality : 0.044 0.306 998 Planarity : 0.004 0.039 1181 Dihedral : 4.697 21.621 866 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.86 % Allowed : 7.86 % Favored : 91.29 % 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: -0.59 (0.31), residues: 793 helix: 0.62 (0.30), residues: 343 sheet: -0.66 (0.65), residues: 60 loop : -1.26 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 306 TYR 0.013 0.001 TYR A 453 PHE 0.009 0.001 PHE F 369 TRP 0.012 0.001 TRP F 473 HIS 0.004 0.001 HIS F 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 6792) covalent geometry : angle 0.61521 / 0.31 ( 9231) SS BOND : bond 0.00240 / 0.13 ( 7) SS BOND : angle 3.82857 / 2.53 ( 14) hydrogen bonds : bond 0.04892 / 3.26 ( 240) hydrogen bonds : angle 4.37409 / 3.03 ( 687) link_BETA1-4 : bond 0.00419 / 0.28 ( 3) link_BETA1-4 : angle 1.26215 / 0.73 ( 9) link_NAG-ASN : bond 0.00574 / 0.21 ( 8) link_NAG-ASN : angle 2.68936 / 2.08 ( 24) *********************** 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 92 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8892 (mp) cc_final: 0.8622 (mt) REVERT: F 600 LYS cc_start: 0.6966 (tppt) cc_final: 0.5707 (tmtt) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.0713 time to fit residues: 9.0165 Evaluate side-chains 85 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 0.0670 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 378 HIS F 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121316 restraints weight = 13481.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122965 restraints weight = 10097.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.123826 restraints weight = 6822.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124343 restraints weight = 5557.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.124656 restraints weight = 4980.734| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6810 Z= 0.147 Angle : 0.635 10.106 9278 Z= 0.316 Chirality : 0.044 0.305 998 Planarity : 0.004 0.033 1181 Dihedral : 4.699 20.269 866 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.43 % Allowed : 11.00 % Favored : 87.57 % 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: -0.56 (0.31), residues: 793 helix: 0.64 (0.29), residues: 344 sheet: -0.25 (0.73), residues: 50 loop : -1.30 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 169 TYR 0.015 0.001 TYR A 453 PHE 0.009 0.001 PHE F 369 TRP 0.011 0.001 TRP F 473 HIS 0.004 0.001 HIS F 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 6792) covalent geometry : angle 0.60714 / 0.31 ( 9231) SS BOND : bond 0.00248 / 0.12 ( 7) SS BOND : angle 3.42245 / 2.18 ( 14) hydrogen bonds : bond 0.04683 / 3.09 ( 240) hydrogen bonds : angle 4.25509 / 2.95 ( 687) link_BETA1-4 : bond 0.00557 / 0.37 ( 3) link_BETA1-4 : angle 1.35150 / 0.77 ( 9) link_NAG-ASN : bond 0.00565 / 0.23 ( 8) link_NAG-ASN : angle 2.53775 / 1.94 ( 24) *********************** 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 97 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 222 LEU cc_start: 0.8268 (tp) cc_final: 0.7957 (tt) REVERT: F 406 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: F 600 LYS cc_start: 0.7062 (tppt) cc_final: 0.5740 (tmtt) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.0618 time to fit residues: 8.5283 Evaluate side-chains 92 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN F 378 HIS F 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122159 restraints weight = 13590.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123839 restraints weight = 9857.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124691 restraints weight = 6750.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125544 restraints weight = 5251.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.125575 restraints weight = 4525.583| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6810 Z= 0.120 Angle : 0.616 9.251 9278 Z= 0.303 Chirality : 0.043 0.296 998 Planarity : 0.004 0.033 1181 Dihedral : 4.627 20.550 866 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.86 % Allowed : 13.14 % 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: -0.48 (0.31), residues: 793 helix: 0.72 (0.29), residues: 344 sheet: -0.18 (0.73), residues: 50 loop : -1.27 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 169 TYR 0.012 0.001 TYR A 453 PHE 0.008 0.001 PHE F 369 TRP 0.014 0.001 TRP F 478 HIS 0.014 0.002 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6792) covalent geometry : angle 0.58844 / 0.29 ( 9231) SS BOND : bond 0.00226 / 0.12 ( 7) SS BOND : angle 3.43030 / 2.18 ( 14) hydrogen bonds : bond 0.04198 / 2.75 ( 240) hydrogen bonds : angle 4.14267 / 2.86 ( 687) link_BETA1-4 : bond 0.00425 / 0.29 ( 3) link_BETA1-4 : angle 1.30371 / 0.76 ( 9) link_NAG-ASN : bond 0.00510 / 0.19 ( 8) link_NAG-ASN : angle 2.42782 / 1.86 ( 24) *********************** 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 100 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 222 LEU cc_start: 0.8077 (tp) cc_final: 0.7843 (tt) REVERT: F 406 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6457 (mt-10) REVERT: F 512 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7442 (t80) REVERT: F 600 LYS cc_start: 0.7111 (tppt) cc_final: 0.5778 (tmtt) outliers start: 13 outliers final: 6 residues processed: 96 average time/residue: 0.0630 time to fit residues: 8.8198 Evaluate side-chains 92 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 13 optimal weight: 0.0030 chunk 3 optimal weight: 9.9990 chunk 67 optimal weight: 0.0170 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121467 restraints weight = 13716.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123008 restraints weight = 10176.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124000 restraints weight = 7189.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124566 restraints weight = 5578.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.124866 restraints weight = 4979.305| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 0.042 6810 Z= 0.125 Angle : 0.635 9.960 9278 Z= 0.309 Chirality : 0.044 0.291 998 Planarity : 0.004 0.033 1181 Dihedral : 4.590 19.820 866 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.43 % Allowed : 14.29 % Favored : 83.29 % 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: -0.42 (0.31), residues: 793 helix: 0.80 (0.30), residues: 339 sheet: -0.18 (0.74), residues: 50 loop : -1.26 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 169 TYR 0.012 0.001 TYR A 453 PHE 0.010 0.001 PHE F 504 TRP 0.014 0.001 TRP F 478 HIS 0.007 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 6792) covalent geometry : angle 0.60038 / 0.30 ( 9231) SS BOND : bond 0.00236 / 0.13 ( 7) SS BOND : angle 3.49027 / 2.24 ( 14) hydrogen bonds : bond 0.04095 / 2.67 ( 240) hydrogen bonds : angle 4.09381 / 2.82 ( 687) link_BETA1-4 : bond 0.00408 / 0.28 ( 3) link_BETA1-4 : angle 1.33223 / 0.83 ( 9) link_NAG-ASN : bond 0.00684 / 0.30 ( 8) link_NAG-ASN : angle 3.06699 / 2.10 ( 24) *********************** 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 109 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.5652 (OUTLIER) cc_final: 0.5357 (tt) REVERT: F 406 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: F 449 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7553 (t) REVERT: F 512 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7298 (t80) REVERT: F 600 LYS cc_start: 0.7105 (tppt) cc_final: 0.5741 (tmtt) outliers start: 17 outliers final: 8 residues processed: 103 average time/residue: 0.0555 time to fit residues: 8.3597 Evaluate side-chains 102 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121570 restraints weight = 14046.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123812 restraints weight = 9525.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124912 restraints weight = 6279.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125587 restraints weight = 4814.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.125900 restraints weight = 4268.049| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6810 Z= 0.118 Angle : 0.640 10.256 9278 Z= 0.309 Chirality : 0.044 0.287 998 Planarity : 0.004 0.032 1181 Dihedral : 4.546 19.356 866 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.29 % Allowed : 15.14 % Favored : 82.57 % 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: -0.37 (0.31), residues: 793 helix: 0.83 (0.30), residues: 340 sheet: -0.13 (0.75), residues: 50 loop : -1.22 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.017 0.001 TYR F 279 PHE 0.007 0.001 PHE F 369 TRP 0.015 0.001 TRP F 478 HIS 0.007 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6792) covalent geometry : angle 0.60443 / 0.30 ( 9231) SS BOND : bond 0.00217 / 0.11 ( 7) SS BOND : angle 3.45553 / 2.20 ( 14) hydrogen bonds : bond 0.03955 / 2.58 ( 240) hydrogen bonds : angle 4.02721 / 2.78 ( 687) link_BETA1-4 : bond 0.00417 / 0.28 ( 3) link_BETA1-4 : angle 1.36814 / 0.83 ( 9) link_NAG-ASN : bond 0.00594 / 0.25 ( 8) link_NAG-ASN : angle 3.21455 / 2.36 ( 24) *********************** 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 108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 518 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.5362 (tt) REVERT: F 406 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6552 (mt-10) REVERT: F 449 THR cc_start: 0.7905 (m) cc_final: 0.7568 (t) REVERT: F 512 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7139 (t80) REVERT: F 600 LYS cc_start: 0.7118 (tppt) cc_final: 0.5765 (tmtt) outliers start: 16 outliers final: 7 residues processed: 105 average time/residue: 0.0662 time to fit residues: 9.8493 Evaluate side-chains 97 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121208 restraints weight = 13629.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123139 restraints weight = 10407.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124037 restraints weight = 6823.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124867 restraints weight = 5395.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125117 restraints weight = 4690.715| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6810 Z= 0.125 Angle : 0.641 10.504 9278 Z= 0.311 Chirality : 0.044 0.285 998 Planarity : 0.004 0.033 1181 Dihedral : 4.538 19.912 866 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.29 % Allowed : 15.29 % Favored : 82.43 % 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: -0.33 (0.31), residues: 793 helix: 0.88 (0.30), residues: 340 sheet: -0.09 (0.76), residues: 50 loop : -1.21 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 393 TYR 0.015 0.001 TYR F 279 PHE 0.014 0.001 PHE F 504 TRP 0.018 0.001 TRP F 478 HIS 0.003 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 6792) covalent geometry : angle 0.60950 / 0.30 ( 9231) SS BOND : bond 0.00125 / 0.06 ( 7) SS BOND : angle 3.47075 / 2.19 ( 14) hydrogen bonds : bond 0.04003 / 2.61 ( 240) hydrogen bonds : angle 3.99713 / 2.76 ( 687) link_BETA1-4 : bond 0.00446 / 0.30 ( 3) link_BETA1-4 : angle 1.40038 / 0.84 ( 9) link_NAG-ASN : bond 0.00564 / 0.24 ( 8) link_NAG-ASN : angle 2.83744 / 2.09 ( 24) *********************** 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 104 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 518 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5413 (tt) REVERT: F 222 LEU cc_start: 0.8108 (tp) cc_final: 0.7872 (tt) REVERT: F 406 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: F 449 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7530 (t) REVERT: F 512 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.7037 (t80) REVERT: F 600 LYS cc_start: 0.7137 (tppt) cc_final: 0.5779 (tmtt) outliers start: 16 outliers final: 9 residues processed: 99 average time/residue: 0.0617 time to fit residues: 8.8256 Evaluate side-chains 97 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120432 restraints weight = 13675.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122256 restraints weight = 10287.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123097 restraints weight = 6779.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123976 restraints weight = 5372.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124132 restraints weight = 4615.305| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6810 Z= 0.140 Angle : 0.662 10.642 9278 Z= 0.324 Chirality : 0.044 0.285 998 Planarity : 0.004 0.036 1181 Dihedral : 4.550 19.211 866 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.00 % Allowed : 14.86 % Favored : 82.14 % 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: -0.37 (0.31), residues: 793 helix: 0.87 (0.30), residues: 340 sheet: -0.10 (0.76), residues: 50 loop : -1.26 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.015 0.001 TYR F 279 PHE 0.007 0.001 PHE F 369 TRP 0.024 0.001 TRP F 478 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 6792) covalent geometry : angle 0.63278 / 0.31 ( 9231) SS BOND : bond 0.00255 / 0.14 ( 7) SS BOND : angle 3.60608 / 2.27 ( 14) hydrogen bonds : bond 0.04168 / 2.72 ( 240) hydrogen bonds : angle 4.01089 / 2.76 ( 687) link_BETA1-4 : bond 0.00483 / 0.33 ( 3) link_BETA1-4 : angle 1.45256 / 0.85 ( 9) link_NAG-ASN : bond 0.00570 / 0.27 ( 8) link_NAG-ASN : angle 2.69743 / 2.01 ( 24) *********************** 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 107 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 518 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5436 (tt) REVERT: F 222 LEU cc_start: 0.8105 (tp) cc_final: 0.7875 (tt) REVERT: F 406 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: F 449 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7545 (t) REVERT: F 512 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6947 (t80) REVERT: F 600 LYS cc_start: 0.7267 (tppt) cc_final: 0.5868 (tmtt) outliers start: 21 outliers final: 9 residues processed: 101 average time/residue: 0.0624 time to fit residues: 9.0766 Evaluate side-chains 97 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.0770 chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120805 restraints weight = 13795.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122733 restraints weight = 10317.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123602 restraints weight = 6785.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124263 restraints weight = 5236.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124459 restraints weight = 4660.841| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6810 Z= 0.131 Angle : 0.665 10.712 9278 Z= 0.325 Chirality : 0.044 0.281 998 Planarity : 0.004 0.035 1181 Dihedral : 4.636 29.136 866 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.29 % Allowed : 15.29 % Favored : 82.43 % 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: -0.36 (0.31), residues: 793 helix: 0.89 (0.30), residues: 340 sheet: -0.12 (0.76), residues: 50 loop : -1.26 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.012 0.001 TYR A 453 PHE 0.017 0.001 PHE F 504 TRP 0.030 0.001 TRP F 478 HIS 0.006 0.001 HIS F 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 6792) covalent geometry : angle 0.63494 / 0.31 ( 9231) SS BOND : bond 0.00250 / 0.14 ( 7) SS BOND : angle 3.79320 / 2.40 ( 14) hydrogen bonds : bond 0.04033 / 2.62 ( 240) hydrogen bonds : angle 3.99729 / 2.75 ( 687) link_BETA1-4 : bond 0.00435 / 0.30 ( 3) link_BETA1-4 : angle 1.45276 / 0.86 ( 9) link_NAG-ASN : bond 0.00522 / 0.23 ( 8) link_NAG-ASN : angle 2.57824 / 1.93 ( 24) *********************** 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 103 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5416 (tt) REVERT: F 222 LEU cc_start: 0.8057 (tp) cc_final: 0.7829 (tt) REVERT: F 406 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: F 449 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7615 (t) REVERT: F 512 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6898 (t80) REVERT: F 600 LYS cc_start: 0.7251 (tppt) cc_final: 0.5871 (tmtt) outliers start: 16 outliers final: 9 residues processed: 98 average time/residue: 0.0596 time to fit residues: 8.3985 Evaluate side-chains 98 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121227 restraints weight = 13714.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123283 restraints weight = 10225.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124147 restraints weight = 6488.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125195 restraints weight = 5125.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.125423 restraints weight = 4331.124| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6810 Z= 0.127 Angle : 0.666 10.815 9278 Z= 0.323 Chirality : 0.043 0.278 998 Planarity : 0.004 0.036 1181 Dihedral : 4.571 23.552 866 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.14 % Allowed : 15.71 % Favored : 82.14 % 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: -0.35 (0.31), residues: 793 helix: 0.90 (0.30), residues: 340 sheet: -0.13 (0.76), residues: 50 loop : -1.26 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 393 TYR 0.012 0.001 TYR F 279 PHE 0.007 0.001 PHE F 369 TRP 0.034 0.001 TRP F 478 HIS 0.004 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6792) covalent geometry : angle 0.63869 / 0.31 ( 9231) SS BOND : bond 0.00240 / 0.13 ( 7) SS BOND : angle 3.60469 / 2.28 ( 14) hydrogen bonds : bond 0.03937 / 2.56 ( 240) hydrogen bonds : angle 3.99481 / 2.76 ( 687) link_BETA1-4 : bond 0.00423 / 0.28 ( 3) link_BETA1-4 : angle 1.44059 / 0.86 ( 9) link_NAG-ASN : bond 0.00508 / 0.22 ( 8) link_NAG-ASN : angle 2.49545 / 1.88 ( 24) ********************** 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 104 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5510 (tt) REVERT: F 222 LEU cc_start: 0.8066 (tp) cc_final: 0.7833 (tt) REVERT: F 406 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6714 (mt-10) REVERT: F 449 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7611 (t) REVERT: F 512 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6737 (t80) REVERT: F 600 LYS cc_start: 0.7399 (tppt) cc_final: 0.5921 (tmtt) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.0629 time to fit residues: 8.9855 Evaluate side-chains 102 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121202 restraints weight = 13918.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122929 restraints weight = 9844.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123880 restraints weight = 6921.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124463 restraints weight = 5353.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124713 restraints weight = 4885.423| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6810 Z= 0.137 Angle : 0.677 10.783 9278 Z= 0.329 Chirality : 0.044 0.277 998 Planarity : 0.004 0.037 1181 Dihedral : 4.656 28.764 866 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.00 % Allowed : 16.14 % Favored : 81.86 % 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: -0.42 (0.31), residues: 793 helix: 0.78 (0.29), residues: 348 sheet: 0.08 (0.77), residues: 48 loop : -1.31 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.013 0.001 TYR A 453 PHE 0.016 0.001 PHE F 504 TRP 0.031 0.001 TRP F 478 HIS 0.003 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6792) covalent geometry : angle 0.64936 / 0.32 ( 9231) SS BOND : bond 0.00337 / 0.22 ( 7) SS BOND : angle 3.68187 / 2.33 ( 14) hydrogen bonds : bond 0.04016 / 2.61 ( 240) hydrogen bonds : angle 3.99117 / 2.75 ( 687) link_BETA1-4 : bond 0.00473 / 0.32 ( 3) link_BETA1-4 : angle 1.46592 / 0.86 ( 9) link_NAG-ASN : bond 0.00527 / 0.25 ( 8) link_NAG-ASN : angle 2.49064 / 1.89 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1112.51 seconds wall clock time: 19 minutes 59.90 seconds (1199.90 seconds total)