Starting phenix.real_space_refine on Sat Aug 23 07:52:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xv0_38688/08_2025/8xv0_38688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xv0_38688/08_2025/8xv0_38688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xv0_38688/08_2025/8xv0_38688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xv0_38688/08_2025/8xv0_38688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xv0_38688/08_2025/8xv0_38688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xv0_38688/08_2025/8xv0_38688.map" } resolution = 3.0 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= -0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4904 atoms to isotropic. 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 4241 2.51 5 N 1078 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6633 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" 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: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.73, per 1000 atoms: 0.26 Number of scatterers: 6633 At special positions: 0 Unit cell: (87.435, 86.43, 118.59, 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 1277 8.00 N 1078 7.00 C 4241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 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 524 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 487 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG A 702 " - " ASN A 432 " " NAG B1300 " - " ASN B 343 " " NAG B1301 " - " ASN B 354 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 90 " " NAG F 1 " - " ASN A 103 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 387.1 milliseconds Enol-peptide restraints added in 1.4 microseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 55.9% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.520A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 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 84 through 88 removed outlier: 3.968A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 174 Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 4.117A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.876A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.501A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.782A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.569A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.045A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.977A 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: 3.711A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.345A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) 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 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 533 removed outlier: 3.719A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.511A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.515A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.092A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.651A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.105A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.686A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN B 394 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 515 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 307 hydrogen bonds defined for protein. 879 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: 0.87 Time building geometry restraints manager: 0.86 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: 2083 1.34 - 1.46: 1770 1.46 - 1.58: 2910 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6821 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.554 -0.028 2.00e-02 2.50e+03 1.90e+00 ... (remaining 6816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 8956 1.28 - 2.56: 225 2.56 - 3.84: 57 3.84 - 5.12: 26 5.12 - 6.39: 7 Bond angle restraints: 9271 Sorted by residual: angle pdb=" C PRO A 135 " pdb=" N ASP A 136 " pdb=" CA ASP A 136 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" CA ASP A 136 " pdb=" CB ASP A 136 " pdb=" CG ASP A 136 " ideal model delta sigma weight residual 112.60 114.88 -2.28 1.00e+00 1.00e+00 5.20e+00 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 119.39 -4.99 2.30e+00 1.89e-01 4.70e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.56 6.39 3.00e+00 1.11e-01 4.54e+00 angle pdb=" C3 MAN F 5 " pdb=" C2 MAN F 5 " pdb=" O2 MAN F 5 " ideal model delta sigma weight residual 111.77 105.39 6.38 3.00e+00 1.11e-01 4.52e+00 ... (remaining 9266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 3964 22.00 - 44.00: 220 44.00 - 66.00: 15 66.00 - 88.01: 16 88.01 - 110.01: 9 Dihedral angle restraints: 4224 sinusoidal: 1903 harmonic: 2321 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 524 " pdb=" CB CYS B 524 " ideal model delta sinusoidal sigma weight residual 93.00 8.76 84.24 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -129.66 43.66 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.70 110.01 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 4221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 1008 0.142 - 0.284: 4 0.284 - 0.426: 1 0.426 - 0.569: 0 0.569 - 0.711: 1 Chirality restraints: 1014 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1011 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " -0.018 2.00e-02 2.50e+03 1.73e-02 3.75e+00 pdb=" CG ASN A 103 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 226 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C VAL A 226 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL A 226 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 227 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 241 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C HIS A 241 " 0.028 2.00e-02 2.50e+03 pdb=" O HIS A 241 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 242 " -0.009 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1320 2.77 - 3.31: 6166 3.31 - 3.84: 10591 3.84 - 4.37: 11686 4.37 - 4.90: 20940 Nonbonded interactions: 50703 Sorted by model distance: nonbonded pdb=" OG SER A 563 " pdb=" OE1 GLU A 564 " model vdw 2.242 3.040 nonbonded pdb=" OG SER A 611 " pdb=" O ALA A 614 " model vdw 2.242 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.276 3.120 nonbonded pdb=" O MET A 152 " pdb=" NH1 ARG A 161 " model vdw 2.305 3.120 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.318 3.120 ... (remaining 50698 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 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: 0.030 Process input model: 8.010 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6844 Z= 0.160 Angle : 0.600 8.265 9333 Z= 0.283 Chirality : 0.049 0.711 1014 Planarity : 0.003 0.025 1175 Dihedral : 14.697 110.007 2713 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 1.12 (0.31), residues: 786 helix: 1.87 (0.28), residues: 395 sheet: 1.62 (0.81), residues: 44 loop : -0.71 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 204 TYR 0.023 0.001 TYR A 199 PHE 0.010 0.001 PHE B 347 TRP 0.026 0.001 TRP A 203 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6821) covalent geometry : angle 0.56093 ( 9271) SS BOND : bond 0.00119 ( 7) SS BOND : angle 1.76926 ( 14) hydrogen bonds : bond 0.15650 ( 307) hydrogen bonds : angle 6.12422 ( 879) link_ALPHA1-3 : bond 0.00401 ( 1) link_ALPHA1-3 : angle 1.47651 ( 3) link_ALPHA1-6 : bond 0.00409 ( 1) link_ALPHA1-6 : angle 1.60825 ( 3) link_BETA1-4 : bond 0.00327 ( 6) link_BETA1-4 : angle 1.95543 ( 18) link_NAG-ASN : bond 0.00712 ( 8) link_NAG-ASN : angle 3.60831 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.274 Fit side-chains REVERT: A 37 GLU cc_start: 0.6388 (mt-10) cc_final: 0.5950 (mt-10) REVERT: A 81 GLN cc_start: 0.7959 (mt0) cc_final: 0.7191 (mm110) REVERT: A 182 GLU cc_start: 0.6543 (tt0) cc_final: 0.6203 (mp0) REVERT: A 190 MET cc_start: 0.5700 (tmm) cc_final: 0.5209 (tmm) REVERT: A 231 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6280 (mt-10) REVERT: A 295 ASP cc_start: 0.5526 (m-30) cc_final: 0.5217 (m-30) REVERT: A 441 LYS cc_start: 0.6526 (tttt) cc_final: 0.6256 (ttpp) REVERT: A 546 ASN cc_start: 0.6704 (m110) cc_final: 0.5429 (p0) REVERT: A 579 MET cc_start: 0.7122 (mtm) cc_final: 0.6827 (mtm) REVERT: A 585 LEU cc_start: 0.6637 (mt) cc_final: 0.6426 (mm) REVERT: B 357 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7038 (ttt180) REVERT: B 378 LYS cc_start: 0.6314 (mmtt) cc_final: 0.5556 (tptp) REVERT: B 440 LYS cc_start: 0.7498 (tmtt) cc_final: 0.7255 (mptt) REVERT: B 462 LYS cc_start: 0.7046 (mmtp) cc_final: 0.6711 (mppt) REVERT: B 468 ILE cc_start: 0.8069 (mt) cc_final: 0.7847 (mm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.6352 time to fit residues: 99.7290 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 121 ASN A 210 ASN A 531 GLN B 388 ASN B 486 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.170931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139571 restraints weight = 7952.285| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.05 r_work: 0.3392 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6844 Z= 0.120 Angle : 0.597 9.700 9333 Z= 0.288 Chirality : 0.043 0.315 1014 Planarity : 0.003 0.032 1175 Dihedral : 10.336 76.239 1185 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.45 % Allowed : 10.23 % Favored : 87.32 % 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: 1.32 (0.31), residues: 786 helix: 2.07 (0.27), residues: 399 sheet: 1.56 (0.80), residues: 42 loop : -0.67 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.013 0.001 TYR A 199 PHE 0.011 0.001 PHE B 377 TRP 0.014 0.001 TRP A 203 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6821) covalent geometry : angle 0.54724 ( 9271) SS BOND : bond 0.00135 ( 7) SS BOND : angle 1.51030 ( 14) hydrogen bonds : bond 0.04742 ( 307) hydrogen bonds : angle 4.29247 ( 879) link_ALPHA1-3 : bond 0.01023 ( 1) link_ALPHA1-3 : angle 2.06520 ( 3) link_ALPHA1-6 : bond 0.00692 ( 1) link_ALPHA1-6 : angle 1.96515 ( 3) link_BETA1-4 : bond 0.00541 ( 6) link_BETA1-4 : angle 2.11454 ( 18) link_NAG-ASN : bond 0.01474 ( 8) link_NAG-ASN : angle 4.14424 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8086 (mt0) cc_final: 0.7762 (mm110) REVERT: A 131 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7123 (ttmm) REVERT: A 190 MET cc_start: 0.7307 (tmm) cc_final: 0.6449 (tmm) REVERT: A 295 ASP cc_start: 0.7097 (m-30) cc_final: 0.6775 (m-30) REVERT: A 482 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.6569 (mmm-85) REVERT: A 546 ASN cc_start: 0.7327 (m110) cc_final: 0.6359 (p0) REVERT: B 378 LYS cc_start: 0.7474 (mmtt) cc_final: 0.7225 (tptp) outliers start: 17 outliers final: 5 residues processed: 108 average time/residue: 0.5979 time to fit residues: 67.9024 Evaluate side-chains 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 0.0470 chunk 70 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 287 GLN B 388 ASN B 505 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.170272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138596 restraints weight = 7922.971| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.02 r_work: 0.3360 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6844 Z= 0.116 Angle : 0.562 8.251 9333 Z= 0.275 Chirality : 0.043 0.319 1014 Planarity : 0.003 0.028 1175 Dihedral : 8.858 73.061 1185 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.74 % Allowed : 12.82 % Favored : 84.44 % 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: 1.35 (0.31), residues: 786 helix: 2.06 (0.27), residues: 405 sheet: 1.58 (0.80), residues: 42 loop : -0.67 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.013 0.001 TYR A 385 PHE 0.014 0.001 PHE B 347 TRP 0.009 0.001 TRP A 165 HIS 0.002 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6821) covalent geometry : angle 0.52558 ( 9271) SS BOND : bond 0.00122 ( 7) SS BOND : angle 1.54058 ( 14) hydrogen bonds : bond 0.04871 ( 307) hydrogen bonds : angle 4.13809 ( 879) link_ALPHA1-3 : bond 0.01197 ( 1) link_ALPHA1-3 : angle 1.67683 ( 3) link_ALPHA1-6 : bond 0.00668 ( 1) link_ALPHA1-6 : angle 1.82460 ( 3) link_BETA1-4 : bond 0.00423 ( 6) link_BETA1-4 : angle 2.12990 ( 18) link_NAG-ASN : bond 0.00625 ( 8) link_NAG-ASN : angle 3.23134 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8172 (mt0) cc_final: 0.7847 (mm110) REVERT: A 131 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7184 (ttmm) REVERT: A 190 MET cc_start: 0.7173 (tmm) cc_final: 0.6555 (tmm) REVERT: A 295 ASP cc_start: 0.7164 (m-30) cc_final: 0.6818 (m-30) REVERT: A 527 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: A 546 ASN cc_start: 0.7153 (m110) cc_final: 0.6214 (p0) REVERT: A 571 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: A 600 LYS cc_start: 0.7738 (pttm) cc_final: 0.7428 (pttt) REVERT: B 378 LYS cc_start: 0.7435 (mmtt) cc_final: 0.7234 (tptp) REVERT: B 462 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7503 (mtpt) outliers start: 19 outliers final: 9 residues processed: 97 average time/residue: 0.5207 time to fit residues: 53.2684 Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.0470 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.168909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136480 restraints weight = 7992.598| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.00 r_work: 0.3337 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6844 Z= 0.112 Angle : 0.567 8.043 9333 Z= 0.274 Chirality : 0.043 0.299 1014 Planarity : 0.003 0.028 1175 Dihedral : 7.994 71.041 1185 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.31 % Allowed : 14.27 % Favored : 83.43 % 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 aren not related in a simple way. whole: 1.31 (0.31), residues: 786 helix: 2.05 (0.27), residues: 406 sheet: 1.51 (0.78), residues: 42 loop : -0.71 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 482 TYR 0.011 0.001 TYR A 50 PHE 0.009 0.001 PHE B 347 TRP 0.009 0.001 TRP A 165 HIS 0.002 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 6821) covalent geometry : angle 0.52852 ( 9271) SS BOND : bond 0.00105 ( 7) SS BOND : angle 1.42837 ( 14) hydrogen bonds : bond 0.04535 ( 307) hydrogen bonds : angle 4.15433 ( 879) link_ALPHA1-3 : bond 0.01478 ( 1) link_ALPHA1-3 : angle 1.41714 ( 3) link_ALPHA1-6 : bond 0.00834 ( 1) link_ALPHA1-6 : angle 1.50817 ( 3) link_BETA1-4 : bond 0.00889 ( 6) link_BETA1-4 : angle 2.88481 ( 18) link_NAG-ASN : bond 0.01000 ( 8) link_NAG-ASN : angle 2.99059 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8256 (mt0) cc_final: 0.7840 (mm110) REVERT: A 131 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7180 (ttmt) REVERT: A 190 MET cc_start: 0.7113 (tmm) cc_final: 0.6242 (tmm) REVERT: A 295 ASP cc_start: 0.7077 (m-30) cc_final: 0.6743 (m-30) REVERT: A 546 ASN cc_start: 0.7103 (m110) cc_final: 0.6114 (p0) REVERT: A 600 LYS cc_start: 0.7735 (pttm) cc_final: 0.7422 (pttt) REVERT: B 440 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8270 (mptt) REVERT: B 462 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7485 (mtpt) REVERT: B 468 ILE cc_start: 0.9074 (mm) cc_final: 0.8873 (mm) outliers start: 16 outliers final: 6 residues processed: 91 average time/residue: 0.5133 time to fit residues: 49.4951 Evaluate side-chains 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.132706 restraints weight = 8019.506| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.07 r_work: 0.3273 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6844 Z= 0.139 Angle : 0.582 8.497 9333 Z= 0.284 Chirality : 0.048 0.635 1014 Planarity : 0.003 0.030 1175 Dihedral : 7.463 66.781 1185 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.45 % Allowed : 14.84 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.31), residues: 786 helix: 2.02 (0.27), residues: 405 sheet: 1.44 (0.78), residues: 42 loop : -0.73 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.017 0.001 TYR A 385 PHE 0.017 0.002 PHE B 347 TRP 0.009 0.001 TRP A 165 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6821) covalent geometry : angle 0.54096 ( 9271) SS BOND : bond 0.00160 ( 7) SS BOND : angle 1.61528 ( 14) hydrogen bonds : bond 0.05340 ( 307) hydrogen bonds : angle 4.12160 ( 879) link_ALPHA1-3 : bond 0.01273 ( 1) link_ALPHA1-3 : angle 2.24345 ( 3) link_ALPHA1-6 : bond 0.00783 ( 1) link_ALPHA1-6 : angle 1.75918 ( 3) link_BETA1-4 : bond 0.00310 ( 6) link_BETA1-4 : angle 2.20078 ( 18) link_NAG-ASN : bond 0.00937 ( 8) link_NAG-ASN : angle 3.53983 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.265 Fit side-chains REVERT: A 81 GLN cc_start: 0.8373 (mt0) cc_final: 0.7946 (mm110) REVERT: A 131 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7145 (ttmt) REVERT: A 190 MET cc_start: 0.7160 (tmm) cc_final: 0.6274 (tmm) REVERT: A 295 ASP cc_start: 0.7140 (m-30) cc_final: 0.6799 (m-30) REVERT: A 401 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7683 (m-70) REVERT: A 527 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: A 600 LYS cc_start: 0.7764 (pttm) cc_final: 0.7433 (pttt) REVERT: B 462 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7488 (mtpt) outliers start: 17 outliers final: 9 residues processed: 88 average time/residue: 0.5121 time to fit residues: 47.8105 Evaluate side-chains 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133228 restraints weight = 8024.035| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.31 r_work: 0.3274 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6844 Z= 0.125 Angle : 0.563 8.329 9333 Z= 0.277 Chirality : 0.044 0.380 1014 Planarity : 0.003 0.028 1175 Dihedral : 7.288 67.638 1185 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.74 % Allowed : 15.27 % Favored : 81.99 % 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: 1.27 (0.31), residues: 786 helix: 2.09 (0.27), residues: 399 sheet: 0.98 (0.70), residues: 52 loop : -0.75 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.014 0.001 TYR A 385 PHE 0.012 0.001 PHE B 347 TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6821) covalent geometry : angle 0.52629 ( 9271) SS BOND : bond 0.00297 ( 7) SS BOND : angle 1.72042 ( 14) hydrogen bonds : bond 0.05168 ( 307) hydrogen bonds : angle 4.13684 ( 879) link_ALPHA1-3 : bond 0.01286 ( 1) link_ALPHA1-3 : angle 1.87691 ( 3) link_ALPHA1-6 : bond 0.00670 ( 1) link_ALPHA1-6 : angle 1.46011 ( 3) link_BETA1-4 : bond 0.00534 ( 6) link_BETA1-4 : angle 2.03023 ( 18) link_NAG-ASN : bond 0.00836 ( 8) link_NAG-ASN : angle 3.26344 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8436 (mt0) cc_final: 0.8021 (mm110) REVERT: A 82 MET cc_start: 0.7805 (ttm) cc_final: 0.7562 (mtt) REVERT: A 131 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7245 (ttmt) REVERT: A 190 MET cc_start: 0.7206 (tmm) cc_final: 0.6365 (tmm) REVERT: A 224 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: A 295 ASP cc_start: 0.7265 (m-30) cc_final: 0.6933 (m-30) REVERT: A 376 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7897 (tpt) REVERT: A 401 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7592 (m-70) REVERT: A 527 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: A 546 ASN cc_start: 0.7103 (m110) cc_final: 0.6226 (p0) REVERT: A 600 LYS cc_start: 0.7792 (pttm) cc_final: 0.7460 (pttt) REVERT: B 440 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8211 (mptt) REVERT: B 462 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7453 (mtpt) outliers start: 19 outliers final: 9 residues processed: 90 average time/residue: 0.5224 time to fit residues: 49.7764 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 516 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130453 restraints weight = 7876.180| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.08 r_work: 0.3291 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6844 Z= 0.139 Angle : 0.580 8.766 9333 Z= 0.288 Chirality : 0.045 0.378 1014 Planarity : 0.003 0.030 1175 Dihedral : 7.133 64.995 1185 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.59 % Allowed : 15.99 % Favored : 81.41 % 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: 1.26 (0.31), residues: 786 helix: 2.06 (0.27), residues: 399 sheet: 0.95 (0.71), residues: 52 loop : -0.72 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.016 0.001 TYR A 385 PHE 0.015 0.002 PHE B 347 TRP 0.009 0.001 TRP A 165 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6821) covalent geometry : angle 0.54426 ( 9271) SS BOND : bond 0.00137 ( 7) SS BOND : angle 1.72961 ( 14) hydrogen bonds : bond 0.05610 ( 307) hydrogen bonds : angle 4.16542 ( 879) link_ALPHA1-3 : bond 0.01271 ( 1) link_ALPHA1-3 : angle 1.83568 ( 3) link_ALPHA1-6 : bond 0.00708 ( 1) link_ALPHA1-6 : angle 1.39138 ( 3) link_BETA1-4 : bond 0.00418 ( 6) link_BETA1-4 : angle 1.97733 ( 18) link_NAG-ASN : bond 0.00742 ( 8) link_NAG-ASN : angle 3.31469 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8365 (mt0) cc_final: 0.8012 (mm110) REVERT: A 82 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7703 (mtt) REVERT: A 131 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7204 (ttmt) REVERT: A 190 MET cc_start: 0.7101 (tmm) cc_final: 0.6230 (tmm) REVERT: A 224 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: A 295 ASP cc_start: 0.7178 (m-30) cc_final: 0.6824 (m-30) REVERT: A 401 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7594 (m-70) REVERT: A 527 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: A 546 ASN cc_start: 0.7030 (m110) cc_final: 0.6185 (p0) REVERT: B 462 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7493 (mtpt) outliers start: 18 outliers final: 11 residues processed: 89 average time/residue: 0.5065 time to fit residues: 47.7026 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 516 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.164601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131603 restraints weight = 7910.167| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.07 r_work: 0.3281 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6844 Z= 0.122 Angle : 0.556 8.423 9333 Z= 0.275 Chirality : 0.044 0.346 1014 Planarity : 0.003 0.029 1175 Dihedral : 6.864 61.584 1185 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.88 % Allowed : 15.99 % Favored : 81.12 % 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: 1.25 (0.31), residues: 786 helix: 2.06 (0.27), residues: 398 sheet: 1.03 (0.71), residues: 52 loop : -0.73 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 482 TYR 0.013 0.001 TYR A 385 PHE 0.010 0.001 PHE B 347 TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6821) covalent geometry : angle 0.52059 ( 9271) SS BOND : bond 0.00102 ( 7) SS BOND : angle 1.60306 ( 14) hydrogen bonds : bond 0.05129 ( 307) hydrogen bonds : angle 4.14871 ( 879) link_ALPHA1-3 : bond 0.01199 ( 1) link_ALPHA1-3 : angle 1.79836 ( 3) link_ALPHA1-6 : bond 0.00728 ( 1) link_ALPHA1-6 : angle 1.38343 ( 3) link_BETA1-4 : bond 0.00456 ( 6) link_BETA1-4 : angle 1.89033 ( 18) link_NAG-ASN : bond 0.00684 ( 8) link_NAG-ASN : angle 3.24238 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8406 (mt0) cc_final: 0.8112 (mm110) REVERT: A 114 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7984 (pptt) REVERT: A 131 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7151 (ttmt) REVERT: A 190 MET cc_start: 0.7099 (tmm) cc_final: 0.6244 (tmm) REVERT: A 224 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7046 (mm-30) REVERT: A 295 ASP cc_start: 0.7179 (m-30) cc_final: 0.6822 (m-30) REVERT: A 401 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7554 (m-70) REVERT: A 527 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: A 546 ASN cc_start: 0.6959 (m110) cc_final: 0.6123 (p0) REVERT: A 600 LYS cc_start: 0.7689 (pttm) cc_final: 0.7394 (pttt) REVERT: B 440 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8156 (mmtm) REVERT: B 462 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7429 (mtpt) outliers start: 20 outliers final: 9 residues processed: 90 average time/residue: 0.4727 time to fit residues: 45.2974 Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 516 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 0.0670 chunk 26 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133426 restraints weight = 7973.836| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.08 r_work: 0.3308 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6844 Z= 0.109 Angle : 0.542 7.770 9333 Z= 0.266 Chirality : 0.043 0.330 1014 Planarity : 0.003 0.027 1175 Dihedral : 6.520 56.997 1185 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.31 % Allowed : 16.57 % Favored : 81.12 % 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: 1.28 (0.31), residues: 786 helix: 2.06 (0.27), residues: 400 sheet: 1.08 (0.70), residues: 52 loop : -0.72 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.010 0.001 TYR A 385 PHE 0.009 0.001 PHE A 315 TRP 0.011 0.001 TRP A 165 HIS 0.002 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6821) covalent geometry : angle 0.51032 ( 9271) SS BOND : bond 0.00076 ( 7) SS BOND : angle 1.47160 ( 14) hydrogen bonds : bond 0.04724 ( 307) hydrogen bonds : angle 4.15310 ( 879) link_ALPHA1-3 : bond 0.01202 ( 1) link_ALPHA1-3 : angle 1.81880 ( 3) link_ALPHA1-6 : bond 0.00834 ( 1) link_ALPHA1-6 : angle 1.42217 ( 3) link_BETA1-4 : bond 0.00442 ( 6) link_BETA1-4 : angle 1.76111 ( 18) link_NAG-ASN : bond 0.00652 ( 8) link_NAG-ASN : angle 3.07654 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8402 (mt0) cc_final: 0.8106 (mm110) REVERT: A 131 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7190 (ttmt) REVERT: A 190 MET cc_start: 0.7090 (tmm) cc_final: 0.6258 (tmm) REVERT: A 224 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7006 (mm-30) REVERT: A 295 ASP cc_start: 0.7158 (m-30) cc_final: 0.6801 (m-30) REVERT: A 401 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7511 (m-70) REVERT: A 527 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: A 546 ASN cc_start: 0.6790 (m110) cc_final: 0.5979 (p0) REVERT: A 600 LYS cc_start: 0.7679 (pttm) cc_final: 0.7379 (pttt) REVERT: B 388 ASN cc_start: 0.7195 (m-40) cc_final: 0.6949 (t0) REVERT: B 440 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8111 (mmtm) REVERT: B 462 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7396 (mtpt) outliers start: 16 outliers final: 7 residues processed: 91 average time/residue: 0.5029 time to fit residues: 48.4602 Evaluate side-chains 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.162232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130229 restraints weight = 7913.539| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.07 r_work: 0.3280 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6844 Z= 0.157 Angle : 0.601 8.246 9333 Z= 0.299 Chirality : 0.046 0.349 1014 Planarity : 0.004 0.035 1175 Dihedral : 6.740 56.490 1185 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.87 % Allowed : 17.15 % Favored : 80.98 % 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: 1.13 (0.31), residues: 786 helix: 1.94 (0.27), residues: 399 sheet: 0.94 (0.70), residues: 52 loop : -0.78 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.016 0.002 TYR A 385 PHE 0.013 0.002 PHE B 342 TRP 0.010 0.001 TRP A 165 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6821) covalent geometry : angle 0.56797 ( 9271) SS BOND : bond 0.00167 ( 7) SS BOND : angle 1.78254 ( 14) hydrogen bonds : bond 0.05994 ( 307) hydrogen bonds : angle 4.22582 ( 879) link_ALPHA1-3 : bond 0.01286 ( 1) link_ALPHA1-3 : angle 1.81530 ( 3) link_ALPHA1-6 : bond 0.00751 ( 1) link_ALPHA1-6 : angle 1.21189 ( 3) link_BETA1-4 : bond 0.00443 ( 6) link_BETA1-4 : angle 2.00151 ( 18) link_NAG-ASN : bond 0.00660 ( 8) link_NAG-ASN : angle 3.24980 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8439 (mt0) cc_final: 0.8146 (mm110) REVERT: A 114 LYS cc_start: 0.8296 (pptt) cc_final: 0.8016 (pptt) REVERT: A 131 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7235 (ttmt) REVERT: A 190 MET cc_start: 0.7159 (tmm) cc_final: 0.6293 (tmm) REVERT: A 295 ASP cc_start: 0.7146 (m-30) cc_final: 0.6759 (m-30) REVERT: A 401 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7628 (m-70) REVERT: A 546 ASN cc_start: 0.7109 (m110) cc_final: 0.6176 (p0) REVERT: A 600 LYS cc_start: 0.7721 (pttm) cc_final: 0.7418 (pttt) REVERT: B 388 ASN cc_start: 0.7321 (m-40) cc_final: 0.6778 (t0) REVERT: B 440 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8107 (mmtm) REVERT: B 462 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7489 (mtpt) outliers start: 13 outliers final: 8 residues processed: 85 average time/residue: 0.5303 time to fit residues: 47.7615 Evaluate side-chains 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.0570 chunk 41 optimal weight: 0.2980 chunk 61 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.0270 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.1556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 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 = 0.168050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136497 restraints weight = 7869.299| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.03 r_work: 0.3308 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6844 Z= 0.103 Angle : 0.532 7.186 9333 Z= 0.260 Chirality : 0.042 0.314 1014 Planarity : 0.003 0.028 1175 Dihedral : 6.102 48.320 1185 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.30 % Allowed : 18.01 % Favored : 80.69 % 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: 1.34 (0.31), residues: 786 helix: 2.13 (0.27), residues: 399 sheet: 1.13 (0.70), residues: 52 loop : -0.70 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.009 0.001 TYR B 494 PHE 0.008 0.001 PHE A 315 TRP 0.014 0.001 TRP A 165 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 6821) covalent geometry : angle 0.50175 ( 9271) SS BOND : bond 0.00066 ( 7) SS BOND : angle 1.37680 ( 14) hydrogen bonds : bond 0.04180 ( 307) hydrogen bonds : angle 4.14421 ( 879) link_ALPHA1-3 : bond 0.01174 ( 1) link_ALPHA1-3 : angle 1.86100 ( 3) link_ALPHA1-6 : bond 0.00877 ( 1) link_ALPHA1-6 : angle 1.36405 ( 3) link_BETA1-4 : bond 0.00484 ( 6) link_BETA1-4 : angle 1.66662 ( 18) link_NAG-ASN : bond 0.00655 ( 8) link_NAG-ASN : angle 2.96454 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.65 seconds wall clock time: 42 minutes 37.24 seconds (2557.24 seconds total)