Starting phenix.real_space_refine on Wed Sep 17 07:08:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yft_39229/09_2025/8yft_39229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yft_39229/09_2025/8yft_39229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yft_39229/09_2025/8yft_39229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yft_39229/09_2025/8yft_39229.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yft_39229/09_2025/8yft_39229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yft_39229/09_2025/8yft_39229.map" } resolution = 3.16 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= -0.002 sd= 0.010 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4164 2.51 5 N 1065 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6508 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4840 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 27, 'TRANS': 561} Chain breaks: 1 Chain: "B" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.45, per 1000 atoms: 0.22 Number of scatterers: 6508 At special positions: 0 Unit cell: (97.98, 74.52, 120.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1242 8.00 N 1065 7.00 C 4164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.06 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 702 " - " ASN A 53 " " NAG C 1 " - " ASN A 216 " " NAG D 1 " - " ASN A 322 " " NAG E 1 " - " ASN A 299 " " NAG F 1 " - " ASN B 343 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 316.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1476 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 54.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 20 through 54 removed outlier: 4.161A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 removed outlier: 3.909A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 103 removed outlier: 3.665A pdb=" N LYS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.699A pdb=" N GLN A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.713A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.517A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.608A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 218 through 230 removed outlier: 4.049A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 removed outlier: 4.044A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.962A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.856A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.390A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.846A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.921A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.661A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.952A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 534 removed outlier: 3.627A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.845A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.907A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.841A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.290A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.848A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.134A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 359 removed outlier: 4.119A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 257 hydrogen bonds defined for protein. 732 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: 0.81 Time building geometry restraints manager: 0.53 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: 2055 1.34 - 1.46: 1751 1.46 - 1.58: 2830 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 6693 Sorted by residual: bond pdb=" CA TYR A 243 " pdb=" C TYR A 243 " ideal model delta sigma weight residual 1.524 1.457 0.068 1.28e-02 6.10e+03 2.80e+01 bond pdb=" N PHE B 486 " pdb=" CA PHE B 486 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.31e-02 5.83e+03 9.58e+00 bond pdb=" N ARG B 346 " pdb=" CA ARG B 346 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.23e-02 6.61e+03 8.56e+00 bond pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.50e+00 bond pdb=" N CYS B 488 " pdb=" CA CYS B 488 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.25e-02 6.40e+03 7.16e+00 ... (remaining 6688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 8862 1.83 - 3.66: 196 3.66 - 5.49: 31 5.49 - 7.32: 4 7.32 - 9.15: 3 Bond angle restraints: 9096 Sorted by residual: angle pdb=" N PHE B 486 " pdb=" CA PHE B 486 " pdb=" CB PHE B 486 " ideal model delta sigma weight residual 110.45 119.60 -9.15 1.52e+00 4.33e-01 3.62e+01 angle pdb=" C TYR A 243 " pdb=" CA TYR A 243 " pdb=" CB TYR A 243 " ideal model delta sigma weight residual 110.92 103.31 7.61 1.59e+00 3.96e-01 2.29e+01 angle pdb=" C ASN B 487 " pdb=" CA ASN B 487 " pdb=" CB ASN B 487 " ideal model delta sigma weight residual 110.42 118.49 -8.07 1.99e+00 2.53e-01 1.65e+01 angle pdb=" CA CYS B 488 " pdb=" C CYS B 488 " pdb=" O CYS B 488 " ideal model delta sigma weight residual 120.66 116.08 4.58 1.15e+00 7.56e-01 1.59e+01 angle pdb=" N GLY B 381 " pdb=" CA GLY B 381 " pdb=" C GLY B 381 " ideal model delta sigma weight residual 115.08 108.96 6.12 1.54e+00 4.22e-01 1.58e+01 ... (remaining 9091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3724 17.78 - 35.56: 266 35.56 - 53.34: 35 53.34 - 71.12: 21 71.12 - 88.90: 8 Dihedral angle restraints: 4054 sinusoidal: 1751 harmonic: 2303 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 14.36 78.64 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 34.76 58.24 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" C TYR A 243 " pdb=" N TYR A 243 " pdb=" CA TYR A 243 " pdb=" CB TYR A 243 " ideal model delta harmonic sigma weight residual -122.60 -111.26 -11.34 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 965 0.184 - 0.367: 4 0.367 - 0.551: 0 0.551 - 0.734: 0 0.734 - 0.918: 1 Chirality restraints: 970 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.34e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.83e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.69e+01 ... (remaining 967 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.270 2.00e-02 2.50e+03 2.32e-01 6.73e+02 pdb=" C7 NAG D 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.406 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.241 2.00e-02 2.50e+03 2.04e-01 5.21e+02 pdb=" C7 NAG F 2 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.349 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 702 " -0.150 2.00e-02 2.50e+03 1.25e-01 1.96e+02 pdb=" C7 NAG A 702 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A 702 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG A 702 " 0.206 2.00e-02 2.50e+03 pdb=" O7 NAG A 702 " 0.015 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1519 2.79 - 3.32: 5929 3.32 - 3.84: 9918 3.84 - 4.37: 11416 4.37 - 4.90: 19745 Nonbonded interactions: 48527 Sorted by model distance: nonbonded pdb=" OG1 THR A 365 " pdb=" OD1 ASP A 367 " model vdw 2.261 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.274 3.040 nonbonded pdb=" O ASN A 121 " pdb=" OG1 THR A 125 " model vdw 2.313 3.040 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.317 2.230 nonbonded pdb=" NH1 ARG A 245 " pdb=" O GLY A 605 " model vdw 2.368 3.120 ... (remaining 48522 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 'F' } 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: 14.330 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.530 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 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 0.068 6710 Z= 0.216 Angle : 0.709 15.822 9135 Z= 0.369 Chirality : 0.055 0.918 970 Planarity : 0.011 0.232 1161 Dihedral : 13.011 88.897 2560 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.12 % Favored : 95.62 % Rotamer: Outliers : 0.58 % Allowed : 0.29 % Favored : 99.13 % Cbeta Deviations : 0.27 % 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 aren not related in a simple way. whole: -0.17 (0.31), residues: 777 helix: 0.83 (0.29), residues: 340 sheet: 2.14 (0.93), residues: 38 loop : -1.21 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.011 0.001 TYR B 501 PHE 0.008 0.001 PHE B 377 TRP 0.022 0.001 TRP A 566 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6693) covalent geometry : angle 0.62820 ( 9096) SS BOND : bond 0.01076 ( 6) SS BOND : angle 1.62174 ( 12) hydrogen bonds : bond 0.20650 ( 257) hydrogen bonds : angle 6.67874 ( 732) metal coordination : bond 0.03116 ( 2) link_BETA1-4 : bond 0.04087 ( 4) link_BETA1-4 : angle 5.83911 ( 12) link_NAG-ASN : bond 0.01552 ( 5) link_NAG-ASN : angle 6.10659 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.7906 (mmp) cc_final: 0.7605 (mmt) REVERT: B 467 ASP cc_start: 0.6675 (t0) cc_final: 0.6316 (t0) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.1116 time to fit residues: 19.7007 Evaluate side-chains 73 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 382 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.082030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.069505 restraints weight = 33308.456| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 8.38 r_work: 0.3457 rms_B_bonded: 8.06 restraints_weight: 2.0000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6710 Z= 0.148 Angle : 0.664 7.242 9135 Z= 0.326 Chirality : 0.043 0.237 970 Planarity : 0.004 0.050 1161 Dihedral : 7.721 57.913 1047 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 2.03 % Allowed : 7.39 % Favored : 90.58 % 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 aren not related in a simple way. whole: 0.31 (0.31), residues: 777 helix: 1.27 (0.29), residues: 345 sheet: 1.87 (0.88), residues: 38 loop : -0.95 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 582 TYR 0.018 0.001 TYR A 243 PHE 0.043 0.001 PHE A 525 TRP 0.014 0.001 TRP A 594 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6693) covalent geometry : angle 0.65059 ( 9096) SS BOND : bond 0.00328 ( 6) SS BOND : angle 0.79673 ( 12) hydrogen bonds : bond 0.04725 ( 257) hydrogen bonds : angle 4.60542 ( 732) metal coordination : bond 0.00187 ( 2) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 2.15523 ( 12) link_NAG-ASN : bond 0.00218 ( 5) link_NAG-ASN : angle 2.79656 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9316 (mt) cc_final: 0.9025 (mt) REVERT: A 462 MET cc_start: 0.9436 (tpp) cc_final: 0.9158 (tpp) REVERT: A 474 MET cc_start: 0.8870 (mmp) cc_final: 0.8291 (mmt) REVERT: B 358 ILE cc_start: 0.8370 (mm) cc_final: 0.8016 (mm) outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 0.1204 time to fit residues: 13.3995 Evaluate side-chains 70 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 465 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 71 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 76 optimal weight: 0.0270 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.0010 chunk 11 optimal weight: 10.0000 overall best weight: 0.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.081727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.069122 restraints weight = 33837.980| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 9.21 r_work: 0.3450 rms_B_bonded: 8.19 restraints_weight: 2.0000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6710 Z= 0.110 Angle : 0.620 11.736 9135 Z= 0.296 Chirality : 0.042 0.195 970 Planarity : 0.004 0.031 1161 Dihedral : 7.602 57.078 1046 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.40 % Rotamer: Outliers : 1.16 % Allowed : 9.42 % Favored : 89.42 % 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 aren not related in a simple way. whole: 0.34 (0.31), residues: 777 helix: 1.18 (0.28), residues: 359 sheet: 1.62 (0.87), residues: 38 loop : -0.85 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 115 TYR 0.023 0.001 TYR B 423 PHE 0.023 0.001 PHE A 525 TRP 0.009 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6693) covalent geometry : angle 0.61214 ( 9096) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.63114 ( 12) hydrogen bonds : bond 0.03824 ( 257) hydrogen bonds : angle 4.35480 ( 732) metal coordination : bond 0.00021 ( 2) link_BETA1-4 : bond 0.00475 ( 4) link_BETA1-4 : angle 1.91603 ( 12) link_NAG-ASN : bond 0.00244 ( 5) link_NAG-ASN : angle 1.98841 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9361 (mt) cc_final: 0.9032 (tt) REVERT: A 332 MET cc_start: 0.9117 (tmm) cc_final: 0.8892 (tmm) REVERT: A 462 MET cc_start: 0.9497 (tpp) cc_final: 0.9268 (tpp) REVERT: A 474 MET cc_start: 0.8954 (mmp) cc_final: 0.8454 (mmp) REVERT: B 358 ILE cc_start: 0.8326 (mm) cc_final: 0.8051 (mm) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.0887 time to fit residues: 8.9566 Evaluate side-chains 63 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 418 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.079553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.067476 restraints weight = 34412.623| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 8.10 r_work: 0.3430 rms_B_bonded: 7.59 restraints_weight: 2.0000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6710 Z= 0.132 Angle : 0.578 8.220 9135 Z= 0.283 Chirality : 0.041 0.180 970 Planarity : 0.003 0.032 1161 Dihedral : 7.676 58.236 1046 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.65 % Rotamer: Outliers : 1.88 % Allowed : 9.28 % Favored : 88.84 % 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 aren not related in a simple way. whole: 0.26 (0.31), residues: 777 helix: 1.11 (0.28), residues: 362 sheet: 1.47 (0.90), residues: 38 loop : -0.89 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.014 0.001 TYR B 423 PHE 0.018 0.001 PHE A 525 TRP 0.018 0.001 TRP A 302 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6693) covalent geometry : angle 0.57033 ( 9096) SS BOND : bond 0.00394 ( 6) SS BOND : angle 0.84301 ( 12) hydrogen bonds : bond 0.03644 ( 257) hydrogen bonds : angle 4.23528 ( 732) metal coordination : bond 0.00123 ( 2) link_BETA1-4 : bond 0.00264 ( 4) link_BETA1-4 : angle 1.71303 ( 12) link_NAG-ASN : bond 0.00219 ( 5) link_NAG-ASN : angle 1.87847 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9366 (mt) cc_final: 0.9054 (mt) REVERT: A 332 MET cc_start: 0.9115 (tmm) cc_final: 0.8908 (tmm) REVERT: A 462 MET cc_start: 0.9460 (tpp) cc_final: 0.9247 (tpp) REVERT: A 474 MET cc_start: 0.8899 (mmp) cc_final: 0.8405 (mmp) REVERT: B 358 ILE cc_start: 0.8358 (mm) cc_final: 0.8025 (mm) REVERT: B 398 ASP cc_start: 0.7294 (t0) cc_final: 0.6899 (p0) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.0699 time to fit residues: 7.1553 Evaluate side-chains 67 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.0070 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 overall best weight: 0.5692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.079461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.067144 restraints weight = 34136.085| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 8.19 r_work: 0.3424 rms_B_bonded: 7.87 restraints_weight: 2.0000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6710 Z= 0.108 Angle : 0.593 12.250 9135 Z= 0.277 Chirality : 0.041 0.191 970 Planarity : 0.003 0.031 1161 Dihedral : 7.629 59.569 1046 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 2.03 % Allowed : 10.14 % Favored : 87.83 % 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 aren not related in a simple way. whole: 0.33 (0.31), residues: 777 helix: 1.17 (0.28), residues: 361 sheet: 1.49 (0.92), residues: 38 loop : -0.85 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.014 0.001 TYR B 423 PHE 0.014 0.001 PHE A 525 TRP 0.015 0.001 TRP A 302 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6693) covalent geometry : angle 0.58562 ( 9096) SS BOND : bond 0.00348 ( 6) SS BOND : angle 0.85513 ( 12) hydrogen bonds : bond 0.03414 ( 257) hydrogen bonds : angle 4.13906 ( 732) metal coordination : bond 0.00073 ( 2) link_BETA1-4 : bond 0.00356 ( 4) link_BETA1-4 : angle 1.66673 ( 12) link_NAG-ASN : bond 0.00175 ( 5) link_NAG-ASN : angle 1.75674 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9387 (mt) cc_final: 0.9065 (mt) REVERT: A 332 MET cc_start: 0.9105 (tmm) cc_final: 0.8894 (tmm) REVERT: A 462 MET cc_start: 0.9506 (tpp) cc_final: 0.9292 (tpp) REVERT: A 474 MET cc_start: 0.8935 (mmp) cc_final: 0.8464 (mmp) REVERT: B 358 ILE cc_start: 0.8400 (mm) cc_final: 0.8071 (mm) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 0.0659 time to fit residues: 6.9477 Evaluate side-chains 67 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.076247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.065130 restraints weight = 35340.754| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 7.50 r_work: 0.3368 rms_B_bonded: 7.36 restraints_weight: 2.0000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6710 Z= 0.189 Angle : 0.629 10.163 9135 Z= 0.308 Chirality : 0.042 0.210 970 Planarity : 0.004 0.036 1161 Dihedral : 7.643 54.059 1046 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.02 % Favored : 94.85 % Rotamer: Outliers : 2.61 % Allowed : 10.29 % Favored : 87.10 % 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 aren not related in a simple way. whole: 0.31 (0.31), residues: 777 helix: 1.20 (0.28), residues: 361 sheet: 1.45 (0.91), residues: 38 loop : -0.92 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 357 TYR 0.016 0.001 TYR A 50 PHE 0.013 0.001 PHE A 588 TRP 0.012 0.001 TRP A 302 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6693) covalent geometry : angle 0.61989 ( 9096) SS BOND : bond 0.00785 ( 6) SS BOND : angle 1.65949 ( 12) hydrogen bonds : bond 0.03870 ( 257) hydrogen bonds : angle 4.33383 ( 732) metal coordination : bond 0.00244 ( 2) link_BETA1-4 : bond 0.00196 ( 4) link_BETA1-4 : angle 1.60417 ( 12) link_NAG-ASN : bond 0.00419 ( 5) link_NAG-ASN : angle 1.95736 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.9450 (mmm) cc_final: 0.9078 (mmm) REVERT: A 267 LEU cc_start: 0.9422 (mt) cc_final: 0.9100 (mt) REVERT: A 332 MET cc_start: 0.9181 (tmm) cc_final: 0.8939 (tmm) REVERT: A 474 MET cc_start: 0.8881 (mmp) cc_final: 0.8413 (mmp) REVERT: B 358 ILE cc_start: 0.8590 (mm) cc_final: 0.8256 (mm) REVERT: B 398 ASP cc_start: 0.7226 (t0) cc_final: 0.6702 (m-30) outliers start: 18 outliers final: 15 residues processed: 73 average time/residue: 0.0735 time to fit residues: 7.7218 Evaluate side-chains 71 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.077250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.066181 restraints weight = 34231.687| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 7.38 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6710 Z= 0.111 Angle : 0.588 10.654 9135 Z= 0.279 Chirality : 0.040 0.181 970 Planarity : 0.003 0.031 1161 Dihedral : 7.582 55.108 1046 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.12 % Favored : 95.75 % Rotamer: Outliers : 2.03 % Allowed : 11.01 % Favored : 86.96 % 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 aren not related in a simple way. whole: 0.49 (0.32), residues: 777 helix: 1.39 (0.29), residues: 356 sheet: 1.54 (0.90), residues: 38 loop : -0.83 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 408 TYR 0.011 0.001 TYR A 50 PHE 0.012 0.001 PHE A 525 TRP 0.016 0.001 TRP A 302 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6693) covalent geometry : angle 0.58162 ( 9096) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.04561 ( 12) hydrogen bonds : bond 0.03365 ( 257) hydrogen bonds : angle 4.15699 ( 732) metal coordination : bond 0.00115 ( 2) link_BETA1-4 : bond 0.00387 ( 4) link_BETA1-4 : angle 1.56440 ( 12) link_NAG-ASN : bond 0.00167 ( 5) link_NAG-ASN : angle 1.71574 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9261 (mmm) cc_final: 0.8876 (mmm) REVERT: A 267 LEU cc_start: 0.9324 (mt) cc_final: 0.9087 (mt) REVERT: A 474 MET cc_start: 0.8360 (mmp) cc_final: 0.7954 (mmp) REVERT: B 358 ILE cc_start: 0.8554 (mm) cc_final: 0.8270 (mm) outliers start: 14 outliers final: 13 residues processed: 71 average time/residue: 0.0689 time to fit residues: 7.2031 Evaluate side-chains 69 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.075261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.064383 restraints weight = 34790.593| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 7.20 r_work: 0.3353 rms_B_bonded: 7.20 restraints_weight: 2.0000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6710 Z= 0.187 Angle : 0.631 10.139 9135 Z= 0.307 Chirality : 0.040 0.169 970 Planarity : 0.004 0.039 1161 Dihedral : 7.664 54.337 1046 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 2.75 % Allowed : 10.72 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: 0.34 (0.31), residues: 777 helix: 1.22 (0.29), residues: 367 sheet: 0.81 (0.87), residues: 40 loop : -0.85 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.015 0.001 TYR A 50 PHE 0.010 0.001 PHE A 525 TRP 0.012 0.001 TRP A 163 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 6693) covalent geometry : angle 0.62265 ( 9096) SS BOND : bond 0.00687 ( 6) SS BOND : angle 1.63268 ( 12) hydrogen bonds : bond 0.03630 ( 257) hydrogen bonds : angle 4.24423 ( 732) metal coordination : bond 0.00191 ( 2) link_BETA1-4 : bond 0.00198 ( 4) link_BETA1-4 : angle 1.56470 ( 12) link_NAG-ASN : bond 0.00423 ( 5) link_NAG-ASN : angle 1.87762 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9435 (mmm) cc_final: 0.9092 (mmm) REVERT: A 297 MET cc_start: 0.8043 (mmm) cc_final: 0.7796 (tpt) REVERT: A 474 MET cc_start: 0.8841 (mmp) cc_final: 0.8422 (mmp) REVERT: B 358 ILE cc_start: 0.8644 (mm) cc_final: 0.8296 (mm) outliers start: 19 outliers final: 15 residues processed: 70 average time/residue: 0.0709 time to fit residues: 7.2969 Evaluate side-chains 69 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.076319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.065272 restraints weight = 35064.025| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 7.46 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6710 Z= 0.115 Angle : 0.619 11.057 9135 Z= 0.291 Chirality : 0.040 0.177 970 Planarity : 0.003 0.030 1161 Dihedral : 7.591 54.630 1046 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 1.88 % Allowed : 12.03 % Favored : 86.09 % 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 aren not related in a simple way. whole: 0.40 (0.31), residues: 777 helix: 1.29 (0.28), residues: 369 sheet: 0.90 (0.87), residues: 40 loop : -0.88 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.011 0.001 TYR B 423 PHE 0.010 0.001 PHE A 525 TRP 0.016 0.001 TRP A 275 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6693) covalent geometry : angle 0.61340 ( 9096) SS BOND : bond 0.00418 ( 6) SS BOND : angle 1.02923 ( 12) hydrogen bonds : bond 0.03411 ( 257) hydrogen bonds : angle 4.11910 ( 732) metal coordination : bond 0.00115 ( 2) link_BETA1-4 : bond 0.00305 ( 4) link_BETA1-4 : angle 1.53882 ( 12) link_NAG-ASN : bond 0.00166 ( 5) link_NAG-ASN : angle 1.63170 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9238 (mmm) cc_final: 0.8903 (mmm) REVERT: A 474 MET cc_start: 0.8315 (mmp) cc_final: 0.7951 (mmp) REVERT: B 358 ILE cc_start: 0.8604 (mm) cc_final: 0.8309 (mm) outliers start: 13 outliers final: 12 residues processed: 67 average time/residue: 0.0688 time to fit residues: 6.7155 Evaluate side-chains 66 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.076199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.064262 restraints weight = 33940.176| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 8.31 r_work: 0.3358 rms_B_bonded: 7.61 restraints_weight: 2.0000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6710 Z= 0.122 Angle : 0.607 10.656 9135 Z= 0.289 Chirality : 0.040 0.172 970 Planarity : 0.003 0.037 1161 Dihedral : 7.563 54.315 1046 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.02 % Favored : 94.85 % Rotamer: Outliers : 1.59 % Allowed : 12.61 % Favored : 85.80 % 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 aren not related in a simple way. whole: 0.41 (0.31), residues: 777 helix: 1.29 (0.28), residues: 377 sheet: 0.95 (0.88), residues: 40 loop : -0.91 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.011 0.001 TYR A 50 PHE 0.010 0.001 PHE A 525 TRP 0.017 0.001 TRP A 302 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6693) covalent geometry : angle 0.60119 ( 9096) SS BOND : bond 0.00466 ( 6) SS BOND : angle 1.03469 ( 12) hydrogen bonds : bond 0.03308 ( 257) hydrogen bonds : angle 4.08058 ( 732) metal coordination : bond 0.00094 ( 2) link_BETA1-4 : bond 0.00300 ( 4) link_BETA1-4 : angle 1.48823 ( 12) link_NAG-ASN : bond 0.00207 ( 5) link_NAG-ASN : angle 1.58766 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9441 (mmm) cc_final: 0.9093 (mmm) REVERT: A 297 MET cc_start: 0.8101 (mmm) cc_final: 0.7876 (tpt) REVERT: A 474 MET cc_start: 0.8835 (mmp) cc_final: 0.8397 (mmp) REVERT: B 358 ILE cc_start: 0.8603 (mm) cc_final: 0.8264 (mm) outliers start: 11 outliers final: 11 residues processed: 65 average time/residue: 0.0790 time to fit residues: 7.2180 Evaluate side-chains 66 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 69 optimal weight: 0.0020 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 422 ASN ** 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 = 0.3891 r_free = 0.3891 target = 0.076732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.064646 restraints weight = 35180.043| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 9.43 r_work: 0.3365 rms_B_bonded: 8.06 restraints_weight: 2.0000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6710 Z= 0.101 Angle : 0.608 11.787 9135 Z= 0.284 Chirality : 0.041 0.197 970 Planarity : 0.003 0.030 1161 Dihedral : 7.502 54.363 1046 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 1.74 % Allowed : 12.61 % Favored : 85.65 % 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 aren not related in a simple way. whole: 0.43 (0.31), residues: 777 helix: 1.26 (0.28), residues: 377 sheet: 1.03 (0.90), residues: 40 loop : -0.85 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.011 0.001 TYR B 423 PHE 0.010 0.001 PHE A 525 TRP 0.018 0.001 TRP A 302 HIS 0.002 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6693) covalent geometry : angle 0.60404 ( 9096) SS BOND : bond 0.00307 ( 6) SS BOND : angle 0.68440 ( 12) hydrogen bonds : bond 0.03263 ( 257) hydrogen bonds : angle 3.99665 ( 732) metal coordination : bond 0.00034 ( 2) link_BETA1-4 : bond 0.00418 ( 4) link_BETA1-4 : angle 1.48911 ( 12) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 1.41356 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2726.06 seconds wall clock time: 47 minutes 19.20 seconds (2839.20 seconds total)