Starting phenix.real_space_refine on Sat Aug 23 02:11:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvu_34138/08_2025/7yvu_34138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvu_34138/08_2025/7yvu_34138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yvu_34138/08_2025/7yvu_34138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvu_34138/08_2025/7yvu_34138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvu_34138/08_2025/7yvu_34138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvu_34138/08_2025/7yvu_34138.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 3164 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4124 2.51 5 N 1081 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 6456 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4856 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.67, per 1000 atoms: 0.26 Number of scatterers: 6456 At special positions: 0 Unit cell: (81.07, 90.45, 114.57, 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 37 16.00 O 1213 8.00 N 1081 7.00 C 4124 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=2.04 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=2.03 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 NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 546 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 321.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 378 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 57.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 4.352A pdb=" N ASN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.571A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.597A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.842A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.741A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) 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 221 through 232 removed outlier: 3.713A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.656A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.397A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' 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 283 Proline residue: A 280 - end of helix removed outlier: 4.109A pdb=" N VAL A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.580A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.591A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 411 removed outlier: 3.521A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.839A pdb=" N ILE A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.549A pdb=" N ALA A 501 " --> pdb=" O CYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.571A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.594A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.078A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.810A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 570 " --> pdb=" O TRP A 566 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.608A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.629A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.711A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.041A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.681A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.277A 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 352 removed outlier: 6.059A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.774A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 284 hydrogen bonds defined for protein. 792 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: 0.78 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.48: 1820 1.48 - 1.61: 2680 1.61 - 1.73: 0 1.73 - 1.86: 58 Bond restraints: 6638 Sorted by residual: bond pdb=" CA ASN A 49 " pdb=" C ASN A 49 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.35e-02 5.49e+03 8.43e+00 bond pdb=" N GLU A 402 " pdb=" CA GLU A 402 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.96e+00 bond pdb=" CB PRO B 521 " pdb=" CG PRO B 521 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.41e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.859 -0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 6633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8831 1.97 - 3.94: 158 3.94 - 5.91: 23 5.91 - 7.88: 5 7.88 - 9.84: 1 Bond angle restraints: 9018 Sorted by residual: angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 113.20 108.38 4.82 9.60e-01 1.09e+00 2.52e+01 angle pdb=" C ASP A 509 " pdb=" CA ASP A 509 " pdb=" CB ASP A 509 " ideal model delta sigma weight residual 116.34 110.19 6.15 1.40e+00 5.10e-01 1.93e+01 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 121.80 131.64 -9.84 2.44e+00 1.68e-01 1.63e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.14 114.18 -6.04 1.52e+00 4.33e-01 1.58e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 121.85 -7.45 2.30e+00 1.89e-01 1.05e+01 ... (remaining 9013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 3518 17.49 - 34.98: 355 34.98 - 52.46: 66 52.46 - 69.95: 16 69.95 - 87.44: 10 Dihedral angle restraints: 3965 sinusoidal: 1640 harmonic: 2325 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.96 -59.96 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 42.17 50.83 1 1.00e+01 1.00e-02 3.54e+01 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 93.00 129.29 -36.29 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 3962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 609 0.037 - 0.073: 235 0.073 - 0.110: 73 0.110 - 0.147: 23 0.147 - 0.183: 3 Chirality restraints: 943 Sorted by residual: chirality pdb=" CA PRO B 521 " pdb=" N PRO B 521 " pdb=" C PRO B 521 " pdb=" CB PRO B 521 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" C2 NAG A 701 " pdb=" C1 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" N2 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA CYS B 432 " pdb=" N CYS B 432 " pdb=" C CYS B 432 " pdb=" CB CYS B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 940 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO B 521 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 146 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 252 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO A 253 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.032 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 77 2.66 - 3.22: 6007 3.22 - 3.78: 9260 3.78 - 4.34: 12549 4.34 - 4.90: 21450 Nonbonded interactions: 49343 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 703 " model vdw 2.103 2.230 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.153 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.253 3.120 nonbonded pdb=" O PRO B 384 " pdb=" OG1 THR B 385 " model vdw 2.292 3.040 ... (remaining 49338 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9.330 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.780 Find NCS groups from input model: 0.010 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.005 0.167 6650 Z= 0.209 Angle : 0.641 9.844 9041 Z= 0.343 Chirality : 0.045 0.183 943 Planarity : 0.007 0.117 1169 Dihedral : 14.813 87.438 2452 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.46 % Favored : 94.03 % Rotamer: Outliers : 0.29 % Allowed : 0.44 % Favored : 99.27 % 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: -0.60 (0.30), residues: 787 helix: 0.61 (0.28), residues: 388 sheet: 0.04 (0.71), residues: 50 loop : -1.64 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 246 TYR 0.017 0.001 TYR A 381 PHE 0.023 0.001 PHE A 308 TRP 0.028 0.002 TRP A 594 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6638) covalent geometry : angle 0.63556 ( 9018) SS BOND : bond 0.00558 ( 7) SS BOND : angle 1.58627 ( 14) hydrogen bonds : bond 0.17931 ( 284) hydrogen bonds : angle 6.07070 ( 792) metal coordination : bond 0.16530 ( 2) link_NAG-ASN : bond 0.00293 ( 3) link_NAG-ASN : angle 1.96507 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.242 Fit side-chains REVERT: A 78 LYS cc_start: 0.8354 (tptm) cc_final: 0.8014 (tptm) REVERT: A 216 ASN cc_start: 0.7667 (m-40) cc_final: 0.7430 (m-40) REVERT: A 402 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6352 (mm-30) REVERT: A 421 ILE cc_start: 0.8013 (tp) cc_final: 0.7812 (tp) REVERT: A 455 MET cc_start: 0.7398 (tmm) cc_final: 0.6952 (tmm) REVERT: A 479 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 508 ASN cc_start: 0.7589 (m-40) cc_final: 0.7296 (t0) REVERT: B 357 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7901 (ttp80) REVERT: B 438 SER cc_start: 0.7762 (t) cc_final: 0.7441 (t) REVERT: B 443 SER cc_start: 0.8240 (m) cc_final: 0.7986 (m) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.0714 time to fit residues: 19.8181 Evaluate side-chains 191 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 374 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104686 restraints weight = 9798.356| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.18 r_work: 0.3198 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 6650 Z= 0.179 Angle : 0.618 10.222 9041 Z= 0.311 Chirality : 0.045 0.272 943 Planarity : 0.007 0.117 1169 Dihedral : 6.176 59.050 932 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.72 % Favored : 93.77 % Rotamer: Outliers : 1.60 % Allowed : 11.35 % Favored : 87.05 % 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: -0.29 (0.30), residues: 787 helix: 0.90 (0.27), residues: 391 sheet: 0.06 (0.69), residues: 50 loop : -1.53 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 465 TYR 0.019 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.015 0.001 TRP A 594 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 6638) covalent geometry : angle 0.61317 ( 9018) SS BOND : bond 0.00518 ( 7) SS BOND : angle 1.37110 ( 14) hydrogen bonds : bond 0.05420 ( 284) hydrogen bonds : angle 4.34929 ( 792) metal coordination : bond 0.12672 ( 2) link_NAG-ASN : bond 0.00363 ( 3) link_NAG-ASN : angle 1.96749 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.7911 (mt) cc_final: 0.7677 (tt) REVERT: A 75 GLU cc_start: 0.8442 (tp30) cc_final: 0.8169 (tp30) REVERT: A 78 LYS cc_start: 0.8617 (tptm) cc_final: 0.8283 (tptm) REVERT: A 87 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7110 (tm-30) REVERT: A 111 ASP cc_start: 0.8289 (m-30) cc_final: 0.8015 (t70) REVERT: A 149 ASP cc_start: 0.8038 (t70) cc_final: 0.7834 (t70) REVERT: A 421 ILE cc_start: 0.8725 (tp) cc_final: 0.8453 (tp) REVERT: A 455 MET cc_start: 0.8459 (tmm) cc_final: 0.8085 (tmm) REVERT: A 470 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8512 (tttp) REVERT: A 479 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 508 ASN cc_start: 0.8107 (m-40) cc_final: 0.7675 (t0) REVERT: A 556 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8246 (mtpp) REVERT: B 347 PHE cc_start: 0.8437 (m-10) cc_final: 0.8143 (m-10) REVERT: B 438 SER cc_start: 0.8085 (t) cc_final: 0.7841 (t) REVERT: B 443 SER cc_start: 0.8491 (m) cc_final: 0.8232 (m) outliers start: 11 outliers final: 7 residues processed: 193 average time/residue: 0.0810 time to fit residues: 20.6878 Evaluate side-chains 191 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.0070 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 overall best weight: 0.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106484 restraints weight = 9736.231| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.19 r_work: 0.3229 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6650 Z= 0.120 Angle : 0.574 10.374 9041 Z= 0.285 Chirality : 0.042 0.264 943 Planarity : 0.006 0.116 1169 Dihedral : 5.761 59.450 929 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.70 % Favored : 94.79 % Rotamer: Outliers : 1.75 % Allowed : 13.68 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.30), residues: 787 helix: 1.03 (0.27), residues: 385 sheet: 0.22 (0.68), residues: 50 loop : -1.53 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.017 0.001 TYR A 535 PHE 0.008 0.001 PHE A 308 TRP 0.011 0.001 TRP A 594 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6638) covalent geometry : angle 0.56977 ( 9018) SS BOND : bond 0.00429 ( 7) SS BOND : angle 1.11377 ( 14) hydrogen bonds : bond 0.04497 ( 284) hydrogen bonds : angle 4.16218 ( 792) metal coordination : bond 0.00216 ( 2) link_NAG-ASN : bond 0.00275 ( 3) link_NAG-ASN : angle 1.85422 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8430 (tp30) cc_final: 0.8148 (tp30) REVERT: A 78 LYS cc_start: 0.8547 (tptm) cc_final: 0.8217 (tptm) REVERT: A 87 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7061 (tm-30) REVERT: A 270 MET cc_start: 0.8922 (tpt) cc_final: 0.8230 (tpt) REVERT: A 287 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8029 (mm-40) REVERT: A 350 ASP cc_start: 0.7574 (p0) cc_final: 0.7367 (p0) REVERT: A 421 ILE cc_start: 0.8654 (tp) cc_final: 0.8413 (tp) REVERT: A 455 MET cc_start: 0.8456 (tmm) cc_final: 0.8098 (tmm) REVERT: A 470 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8459 (tttp) REVERT: A 479 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 508 ASN cc_start: 0.8016 (m-40) cc_final: 0.7691 (t0) REVERT: A 556 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8237 (mtpp) REVERT: B 347 PHE cc_start: 0.8442 (m-10) cc_final: 0.8130 (m-80) REVERT: B 438 SER cc_start: 0.8114 (t) cc_final: 0.7855 (t) REVERT: B 443 SER cc_start: 0.8465 (m) cc_final: 0.8205 (m) outliers start: 12 outliers final: 8 residues processed: 187 average time/residue: 0.0773 time to fit residues: 19.3884 Evaluate side-chains 189 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 66 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103747 restraints weight = 9893.317| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.23 r_work: 0.3183 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6650 Z= 0.175 Angle : 0.610 10.297 9041 Z= 0.308 Chirality : 0.045 0.266 943 Planarity : 0.006 0.118 1169 Dihedral : 5.807 58.451 929 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.72 % Favored : 93.77 % Rotamer: Outliers : 2.62 % Allowed : 14.85 % Favored : 82.53 % 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: -0.22 (0.30), residues: 787 helix: 0.91 (0.27), residues: 392 sheet: -0.01 (0.65), residues: 53 loop : -1.43 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.019 0.001 TYR A 385 PHE 0.013 0.001 PHE A 308 TRP 0.015 0.001 TRP A 477 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 6638) covalent geometry : angle 0.60517 ( 9018) SS BOND : bond 0.00415 ( 7) SS BOND : angle 1.49843 ( 14) hydrogen bonds : bond 0.05325 ( 284) hydrogen bonds : angle 4.20278 ( 792) metal coordination : bond 0.00114 ( 2) link_NAG-ASN : bond 0.00291 ( 3) link_NAG-ASN : angle 1.97996 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8438 (tp30) cc_final: 0.8141 (tp30) REVERT: A 78 LYS cc_start: 0.8602 (tptm) cc_final: 0.8259 (tptm) REVERT: A 270 MET cc_start: 0.8964 (tpt) cc_final: 0.8230 (tpt) REVERT: A 287 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8058 (mm-40) REVERT: A 347 THR cc_start: 0.8352 (p) cc_final: 0.8149 (p) REVERT: A 402 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7374 (mm-30) REVERT: A 455 MET cc_start: 0.8509 (tmm) cc_final: 0.8161 (tmm) REVERT: A 470 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8430 (tttp) REVERT: A 479 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7941 (tm-30) REVERT: A 508 ASN cc_start: 0.7970 (m-40) cc_final: 0.7674 (t0) REVERT: A 556 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8263 (mtpp) REVERT: B 347 PHE cc_start: 0.8448 (m-10) cc_final: 0.8100 (m-80) REVERT: B 438 SER cc_start: 0.8125 (t) cc_final: 0.7835 (t) REVERT: B 443 SER cc_start: 0.8499 (m) cc_final: 0.8256 (m) outliers start: 18 outliers final: 14 residues processed: 189 average time/residue: 0.0760 time to fit residues: 19.3882 Evaluate side-chains 200 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 345 HIS A 601 ASN B 394 ASN B 422 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103928 restraints weight = 9950.321| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.21 r_work: 0.3189 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6650 Z= 0.160 Angle : 0.613 10.313 9041 Z= 0.306 Chirality : 0.044 0.261 943 Planarity : 0.006 0.118 1169 Dihedral : 5.785 58.740 929 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.96 % Favored : 94.54 % Rotamer: Outliers : 2.91 % Allowed : 15.14 % Favored : 81.95 % 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: -0.18 (0.30), residues: 787 helix: 1.03 (0.27), residues: 385 sheet: 0.00 (0.65), residues: 53 loop : -1.49 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 577 TYR 0.018 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.013 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6638) covalent geometry : angle 0.60905 ( 9018) SS BOND : bond 0.00471 ( 7) SS BOND : angle 1.36042 ( 14) hydrogen bonds : bond 0.05040 ( 284) hydrogen bonds : angle 4.18474 ( 792) metal coordination : bond 0.00096 ( 2) link_NAG-ASN : bond 0.00265 ( 3) link_NAG-ASN : angle 1.87827 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8451 (tp30) cc_final: 0.8157 (tp30) REVERT: A 78 LYS cc_start: 0.8607 (tptm) cc_final: 0.8264 (tptm) REVERT: A 114 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7763 (mmtt) REVERT: A 270 MET cc_start: 0.8981 (tpt) cc_final: 0.8301 (tpt) REVERT: A 347 THR cc_start: 0.8372 (p) cc_final: 0.8145 (p) REVERT: A 455 MET cc_start: 0.8483 (tmm) cc_final: 0.8133 (tmm) REVERT: A 470 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8422 (tttp) REVERT: A 479 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 508 ASN cc_start: 0.7974 (m-40) cc_final: 0.7720 (t0) REVERT: A 556 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8267 (mtpp) REVERT: B 438 SER cc_start: 0.8097 (t) cc_final: 0.7862 (t) REVERT: B 443 SER cc_start: 0.8490 (m) cc_final: 0.8244 (m) outliers start: 20 outliers final: 15 residues processed: 192 average time/residue: 0.0770 time to fit residues: 19.9542 Evaluate side-chains 196 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103825 restraints weight = 9999.879| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.24 r_work: 0.3186 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6650 Z= 0.161 Angle : 0.614 10.281 9041 Z= 0.308 Chirality : 0.044 0.259 943 Planarity : 0.006 0.118 1169 Dihedral : 5.795 58.524 929 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.72 % Favored : 93.77 % Rotamer: Outliers : 2.62 % Allowed : 16.59 % Favored : 80.79 % 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: -0.17 (0.30), residues: 787 helix: 0.95 (0.27), residues: 392 sheet: 0.11 (0.66), residues: 53 loop : -1.42 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.020 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.013 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6638) covalent geometry : angle 0.60956 ( 9018) SS BOND : bond 0.00514 ( 7) SS BOND : angle 1.47602 ( 14) hydrogen bonds : bond 0.04999 ( 284) hydrogen bonds : angle 4.17044 ( 792) metal coordination : bond 0.00077 ( 2) link_NAG-ASN : bond 0.00267 ( 3) link_NAG-ASN : angle 1.86196 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8453 (tp30) cc_final: 0.8152 (tp30) REVERT: A 78 LYS cc_start: 0.8622 (tptm) cc_final: 0.8262 (tptm) REVERT: A 111 ASP cc_start: 0.8272 (m-30) cc_final: 0.8043 (t70) REVERT: A 114 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7794 (mmtt) REVERT: A 270 MET cc_start: 0.8988 (tpt) cc_final: 0.8275 (tpt) REVERT: A 347 THR cc_start: 0.8378 (p) cc_final: 0.8157 (p) REVERT: A 376 MET cc_start: 0.8636 (tpp) cc_final: 0.8407 (tpp) REVERT: A 402 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 455 MET cc_start: 0.8490 (tmm) cc_final: 0.8144 (tmm) REVERT: A 470 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8439 (tttp) REVERT: A 479 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 508 ASN cc_start: 0.7974 (m-40) cc_final: 0.7732 (t0) REVERT: A 556 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8254 (mtpp) REVERT: B 438 SER cc_start: 0.8145 (t) cc_final: 0.7887 (t) REVERT: B 443 SER cc_start: 0.8497 (m) cc_final: 0.8249 (m) outliers start: 18 outliers final: 15 residues processed: 187 average time/residue: 0.0790 time to fit residues: 19.9548 Evaluate side-chains 197 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103112 restraints weight = 9852.472| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.20 r_work: 0.3179 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6650 Z= 0.181 Angle : 0.631 10.224 9041 Z= 0.318 Chirality : 0.045 0.260 943 Planarity : 0.006 0.119 1169 Dihedral : 5.844 58.224 929 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.59 % Favored : 93.90 % Rotamer: Outliers : 2.91 % Allowed : 17.03 % Favored : 80.06 % 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: -0.21 (0.30), residues: 787 helix: 0.94 (0.27), residues: 392 sheet: 0.02 (0.63), residues: 53 loop : -1.46 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 514 TYR 0.020 0.001 TYR A 385 PHE 0.014 0.001 PHE A 308 TRP 0.014 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6638) covalent geometry : angle 0.62666 ( 9018) SS BOND : bond 0.00440 ( 7) SS BOND : angle 1.56122 ( 14) hydrogen bonds : bond 0.05346 ( 284) hydrogen bonds : angle 4.20644 ( 792) metal coordination : bond 0.00096 ( 2) link_NAG-ASN : bond 0.00281 ( 3) link_NAG-ASN : angle 1.80726 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8449 (tp30) cc_final: 0.8149 (tp30) REVERT: A 78 LYS cc_start: 0.8642 (tptm) cc_final: 0.8277 (tptm) REVERT: A 114 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7756 (mmtt) REVERT: A 347 THR cc_start: 0.8341 (p) cc_final: 0.8118 (p) REVERT: A 402 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 455 MET cc_start: 0.8490 (tmm) cc_final: 0.8150 (tmm) REVERT: A 479 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 508 ASN cc_start: 0.7939 (m-40) cc_final: 0.7724 (t0) REVERT: A 556 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8259 (mtpp) REVERT: B 368 LEU cc_start: 0.7484 (tp) cc_final: 0.7260 (tt) REVERT: B 438 SER cc_start: 0.8177 (t) cc_final: 0.7889 (t) REVERT: B 443 SER cc_start: 0.8500 (m) cc_final: 0.8252 (m) outliers start: 20 outliers final: 16 residues processed: 192 average time/residue: 0.0801 time to fit residues: 20.6669 Evaluate side-chains 199 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 221 GLN A 345 HIS B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104221 restraints weight = 9870.876| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.19 r_work: 0.3193 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6650 Z= 0.152 Angle : 0.626 10.211 9041 Z= 0.312 Chirality : 0.044 0.257 943 Planarity : 0.006 0.119 1169 Dihedral : 5.783 58.166 929 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.21 % Favored : 94.28 % Rotamer: Outliers : 2.77 % Allowed : 17.90 % Favored : 79.33 % 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: -0.13 (0.30), residues: 787 helix: 1.08 (0.27), residues: 385 sheet: 0.06 (0.65), residues: 53 loop : -1.48 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.019 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6638) covalent geometry : angle 0.62175 ( 9018) SS BOND : bond 0.00426 ( 7) SS BOND : angle 1.53264 ( 14) hydrogen bonds : bond 0.04891 ( 284) hydrogen bonds : angle 4.17266 ( 792) metal coordination : bond 0.00061 ( 2) link_NAG-ASN : bond 0.00278 ( 3) link_NAG-ASN : angle 1.73150 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8458 (tp30) cc_final: 0.8169 (tp30) REVERT: A 78 LYS cc_start: 0.8636 (tptm) cc_final: 0.8272 (tptm) REVERT: A 114 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7730 (mmtt) REVERT: A 427 ASP cc_start: 0.8385 (p0) cc_final: 0.8173 (p0) REVERT: A 435 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7325 (mt-10) REVERT: A 455 MET cc_start: 0.8462 (tmm) cc_final: 0.8103 (tmm) REVERT: A 479 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 508 ASN cc_start: 0.7940 (m-40) cc_final: 0.7735 (t0) REVERT: A 556 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8278 (mtpp) REVERT: B 443 SER cc_start: 0.8480 (m) cc_final: 0.8239 (m) outliers start: 19 outliers final: 17 residues processed: 190 average time/residue: 0.0809 time to fit residues: 20.5566 Evaluate side-chains 194 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 0.0050 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 345 HIS B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104566 restraints weight = 10055.187| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.22 r_work: 0.3198 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6650 Z= 0.145 Angle : 0.621 10.169 9041 Z= 0.311 Chirality : 0.044 0.258 943 Planarity : 0.006 0.119 1169 Dihedral : 5.747 57.938 929 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.21 % Favored : 94.28 % Rotamer: Outliers : 2.91 % Allowed : 17.61 % Favored : 79.48 % 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: -0.09 (0.30), residues: 787 helix: 1.09 (0.27), residues: 385 sheet: 0.16 (0.66), residues: 53 loop : -1.43 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 577 TYR 0.018 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6638) covalent geometry : angle 0.61720 ( 9018) SS BOND : bond 0.00411 ( 7) SS BOND : angle 1.46976 ( 14) hydrogen bonds : bond 0.04731 ( 284) hydrogen bonds : angle 4.13184 ( 792) metal coordination : bond 0.00051 ( 2) link_NAG-ASN : bond 0.00276 ( 3) link_NAG-ASN : angle 1.67402 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8479 (tp30) cc_final: 0.8188 (tp30) REVERT: A 78 LYS cc_start: 0.8638 (tptm) cc_final: 0.8270 (tptm) REVERT: A 114 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7728 (mmtt) REVERT: A 427 ASP cc_start: 0.8388 (p0) cc_final: 0.8171 (p0) REVERT: A 455 MET cc_start: 0.8470 (tmm) cc_final: 0.8128 (tmm) REVERT: A 479 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 508 ASN cc_start: 0.7947 (m-40) cc_final: 0.7742 (t0) REVERT: A 556 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8297 (mtpp) REVERT: B 368 LEU cc_start: 0.7478 (tp) cc_final: 0.7257 (tt) REVERT: B 443 SER cc_start: 0.8461 (m) cc_final: 0.8221 (m) outliers start: 20 outliers final: 18 residues processed: 184 average time/residue: 0.0801 time to fit residues: 19.8906 Evaluate side-chains 193 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 345 HIS B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104910 restraints weight = 9862.556| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.19 r_work: 0.3203 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6650 Z= 0.141 Angle : 0.626 10.117 9041 Z= 0.311 Chirality : 0.044 0.256 943 Planarity : 0.006 0.118 1169 Dihedral : 5.716 57.743 929 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.08 % Favored : 94.41 % Rotamer: Outliers : 2.77 % Allowed : 17.90 % Favored : 79.33 % 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: -0.07 (0.30), residues: 787 helix: 1.09 (0.27), residues: 385 sheet: 0.13 (0.66), residues: 53 loop : -1.40 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 577 TYR 0.018 0.001 TYR A 385 PHE 0.012 0.001 PHE A 308 TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6638) covalent geometry : angle 0.62224 ( 9018) SS BOND : bond 0.00495 ( 7) SS BOND : angle 1.49516 ( 14) hydrogen bonds : bond 0.04626 ( 284) hydrogen bonds : angle 4.12122 ( 792) metal coordination : bond 0.00052 ( 2) link_NAG-ASN : bond 0.00271 ( 3) link_NAG-ASN : angle 1.64311 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8471 (tp30) cc_final: 0.8159 (tp30) REVERT: A 78 LYS cc_start: 0.8613 (tptm) cc_final: 0.8248 (tptm) REVERT: A 114 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7711 (mmtt) REVERT: A 287 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7941 (mm-40) REVERT: A 323 MET cc_start: 0.8437 (mmm) cc_final: 0.8222 (mmt) REVERT: A 347 THR cc_start: 0.8343 (p) cc_final: 0.8119 (p) REVERT: A 427 ASP cc_start: 0.8372 (p0) cc_final: 0.8152 (p0) REVERT: A 455 MET cc_start: 0.8468 (tmm) cc_final: 0.8131 (tmm) REVERT: A 479 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 508 ASN cc_start: 0.7940 (m-40) cc_final: 0.7536 (t0) REVERT: A 510 TYR cc_start: 0.8639 (m-80) cc_final: 0.8292 (m-80) REVERT: A 556 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8261 (mtpp) REVERT: B 368 LEU cc_start: 0.7435 (tp) cc_final: 0.7221 (tt) REVERT: B 443 SER cc_start: 0.8469 (m) cc_final: 0.8231 (m) outliers start: 19 outliers final: 18 residues processed: 182 average time/residue: 0.0815 time to fit residues: 19.8338 Evaluate side-chains 193 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.0050 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105172 restraints weight = 9827.716| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.20 r_work: 0.3208 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6650 Z= 0.134 Angle : 0.621 10.057 9041 Z= 0.307 Chirality : 0.043 0.255 943 Planarity : 0.006 0.118 1169 Dihedral : 5.685 57.546 929 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.96 % Favored : 94.54 % Rotamer: Outliers : 2.62 % Allowed : 18.20 % Favored : 79.18 % 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: -0.03 (0.30), residues: 787 helix: 1.12 (0.27), residues: 385 sheet: 0.07 (0.66), residues: 53 loop : -1.36 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 577 TYR 0.017 0.001 TYR A 385 PHE 0.011 0.001 PHE A 308 TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6638) covalent geometry : angle 0.61691 ( 9018) SS BOND : bond 0.00439 ( 7) SS BOND : angle 1.42621 ( 14) hydrogen bonds : bond 0.04475 ( 284) hydrogen bonds : angle 4.08716 ( 792) metal coordination : bond 0.00043 ( 2) link_NAG-ASN : bond 0.00273 ( 3) link_NAG-ASN : angle 1.58945 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.00 seconds wall clock time: 33 minutes 42.32 seconds (2022.32 seconds total)