Starting phenix.real_space_refine on Sat Jul 26 04:53:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7d_29811/07_2025/8g7d_29811.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7d_29811/07_2025/8g7d_29811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7d_29811/07_2025/8g7d_29811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7d_29811/07_2025/8g7d_29811.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7d_29811/07_2025/8g7d_29811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7d_29811/07_2025/8g7d_29811.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5354 2.51 5 N 1421 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8346 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4129 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 34, 'TRANS': 500} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4161 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 34, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 78 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: 6.06, per 1000 atoms: 0.73 Number of scatterers: 8346 At special positions: 0 Unit cell: (66.518, 81.674, 149.876, 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 36 16.00 O 1535 8.00 N 1421 7.00 C 5354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 521 " 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 A1000 " - " ASN A 98 " " NAG A1001 " - " ASN A 522 " " NAG B1000 " - " ASN B 98 " " NAG B1001 " - " ASN B 522 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 956.6 milliseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 40.5% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.509A pdb=" N ASN A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 232 through 253 removed outlier: 6.204A pdb=" N ALA A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.905A pdb=" N TYR A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.557A pdb=" N ARG A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 332 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.646A pdb=" N LEU A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.871A pdb=" N MET A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 4.582A pdb=" N LYS A 389 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.537A pdb=" N THR A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.633A pdb=" N ARG A 441 " --> pdb=" O TRP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 460 Processing helix chain 'A' and resid 460 through 474 removed outlier: 4.053A pdb=" N TYR A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 524 through 545 Processing helix chain 'A' and resid 594 through 603 Processing helix chain 'A' and resid 603 through 608 removed outlier: 4.072A pdb=" N HIS A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 126 through 134 removed outlier: 3.616A pdb=" N THR B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.768A pdb=" N MET B 195 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 196 " --> pdb=" O GLY B 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 196' Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 232 through 253 removed outlier: 6.596A pdb=" N ALA B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HIS B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 276 Processing helix chain 'B' and resid 303 through 316 removed outlier: 3.708A pdb=" N TYR B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 332 Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.608A pdb=" N LEU B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 370 removed outlier: 3.584A pdb=" N GLN B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 4.550A pdb=" N LYS B 389 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 396 removed outlier: 4.536A pdb=" N GLU B 396 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 416 removed outlier: 3.588A pdb=" N ASP B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.699A pdb=" N ARG B 441 " --> pdb=" O TRP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 460 Processing helix chain 'B' and resid 460 through 474 removed outlier: 3.909A pdb=" N TYR B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 524 through 544 removed outlier: 3.574A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 603 Processing helix chain 'B' and resid 604 through 608 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.310A pdb=" N ARG A 50 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 73 removed outlier: 5.402A pdb=" N LEU A 144 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 209 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU A 212 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N LYS A 177 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N THR A 260 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL A 179 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE A 262 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU A 181 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N SER A 264 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 183 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ILE A 288 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 261 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLN A 290 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY A 263 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET A 378 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N TYR A 481 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 380 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N PHE A 483 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A 382 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.901A pdb=" N ARG B 50 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.654A pdb=" N VAL B 209 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B 212 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS B 177 " --> pdb=" O ARG B 258 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR B 260 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 179 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE B 262 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU B 181 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N SER B 264 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 183 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS B 286 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 259 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE B 288 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 261 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLN B 290 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B 263 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET B 378 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N TYR B 481 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 380 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE B 483 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 382 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N LEU B 581 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE B 480 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE B 583 " --> pdb=" O PHE B 480 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR B 482 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 580 " --> pdb=" O ARG B 590 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 798 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: 2.17 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2725 1.34 - 1.46: 1999 1.46 - 1.58: 3795 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 8577 Sorted by residual: bond pdb=" C1 NAG B1000 " pdb=" O5 NAG B1000 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" CA VAL B 391 " pdb=" CB VAL B 391 " ideal model delta sigma weight residual 1.533 1.549 -0.016 1.19e-02 7.06e+03 1.78e+00 bond pdb=" C1 NAG A1000 " pdb=" O5 NAG A1000 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.55e+00 ... (remaining 8572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 11402 1.36 - 2.72: 225 2.72 - 4.09: 58 4.09 - 5.45: 18 5.45 - 6.81: 3 Bond angle restraints: 11706 Sorted by residual: angle pdb=" CA MET A 446 " pdb=" CB MET A 446 " pdb=" CG MET A 446 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" N GLY B 400 " pdb=" CA GLY B 400 " pdb=" C GLY B 400 " ideal model delta sigma weight residual 111.78 116.97 -5.19 1.69e+00 3.50e-01 9.45e+00 angle pdb=" CA GLU B 445 " pdb=" CB GLU B 445 " pdb=" CG GLU B 445 " ideal model delta sigma weight residual 114.10 119.25 -5.15 2.00e+00 2.50e-01 6.62e+00 angle pdb=" N GLY A 316 " pdb=" CA GLY A 316 " pdb=" C GLY A 316 " ideal model delta sigma weight residual 113.18 118.97 -5.79 2.37e+00 1.78e-01 5.97e+00 angle pdb=" C VAL B 391 " pdb=" CA VAL B 391 " pdb=" CB VAL B 391 " ideal model delta sigma weight residual 111.53 114.62 -3.09 1.30e+00 5.92e-01 5.65e+00 ... (remaining 11701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4574 17.99 - 35.99: 397 35.99 - 53.98: 85 53.98 - 71.98: 12 71.98 - 89.97: 5 Dihedral angle restraints: 5073 sinusoidal: 1975 harmonic: 3098 Sorted by residual: dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 328 " pdb=" CB CYS A 328 " ideal model delta sinusoidal sigma weight residual 93.00 158.61 -65.61 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS A 487 " pdb=" SG CYS A 487 " pdb=" SG CYS A 521 " pdb=" CB CYS A 521 " ideal model delta sinusoidal sigma weight residual 93.00 36.55 56.45 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CB CYS B 487 " pdb=" SG CYS B 487 " pdb=" SG CYS B 521 " pdb=" CB CYS B 521 " ideal model delta sinusoidal sigma weight residual 93.00 49.49 43.51 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 5070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 698 0.026 - 0.052: 374 0.052 - 0.078: 121 0.078 - 0.104: 65 0.104 - 0.130: 28 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CA GLN B 549 " pdb=" N GLN B 549 " pdb=" C GLN B 549 " pdb=" CB GLN B 549 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA PRO A 550 " pdb=" N PRO A 550 " pdb=" C PRO A 550 " pdb=" CB PRO A 550 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CG LEU A 79 " pdb=" CB LEU A 79 " pdb=" CD1 LEU A 79 " pdb=" CD2 LEU A 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1283 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 98 " -0.025 2.00e-02 2.50e+03 2.24e-02 6.26e+00 pdb=" CG ASN B 98 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 98 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 98 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG B1000 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 497 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CG ASP A 497 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP A 497 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 497 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 605 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO A 606 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " -0.018 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1578 2.77 - 3.30: 7474 3.30 - 3.83: 13221 3.83 - 4.37: 15990 4.37 - 4.90: 27997 Nonbonded interactions: 66260 Sorted by model distance: nonbonded pdb=" ND2 ASN A 375 " pdb=" O GLN A 475 " model vdw 2.237 3.120 nonbonded pdb=" ND2 ASN B 60 " pdb=" O MET B 512 " model vdw 2.260 3.120 nonbonded pdb=" O PRO A 65 " pdb=" OG1 THR A 150 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR B 302 " pdb=" OD1 ASP B 363 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR B 188 " pdb=" OG SER B 269 " model vdw 2.308 3.040 ... (remaining 66255 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 'A' and (resid 41 through 61 or (resid 62 and (name N or name CA or name \ C or name O or name CB )) or resid 63 through 226 or (resid 227 through 229 and \ (name N or name CA or name C or name O or name CB )) or resid 230 through 317 or \ (resid 318 through 321 and (name N or name CA or name C or name O or name CB )) \ or resid 322 through 323 or (resid 324 through 325 and (name N or name CA or na \ me C or name O or name CB )) or resid 326 through 361 or (resid 362 and (name N \ or name CA or name C or name O or name CB )) or resid 363 through 398 or (resid \ 399 and (name N or name CA or name C or name O or name CB )) or resid 400 throug \ h 485 or (resid 486 and (name N or name CA or name C or name O or name CB )) or \ resid 487 or (resid 488 through 490 and (name N or name CA or name C or name O o \ r name CB )) or resid 491 through 589 or (resid 590 and (name N or name CA or na \ me C or name O or name CB )) or resid 591 through 608 or resid 1000 through 1001 \ )) selection = (chain 'B' and (resid 41 through 60 or (resid 61 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 391 or (resid 392 throu \ gh 393 and (name N or name CA or name C or name O or name CB )) or resid 394 thr \ ough 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) \ or resid 425 through 441 or (resid 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 524 or (resid 525 and (name \ N or name CA or name C or name O or name CB )) or resid 526 through 548 or (res \ id 549 and (name N or name CA or name C or name O or name CB )) or resid 550 thr \ ough 553 or resid 564 through 565 or (resid 566 through 567 and (name N or name \ CA or name C or name O or name CB )) or resid 568 through 573 or (resid 574 and \ (name N or name CA or name C or name O or name CB )) or resid 575 through 608 or \ resid 1000 through 1001)) } 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.810 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 0.051 8587 Z= 0.138 Angle : 0.536 7.720 11730 Z= 0.265 Chirality : 0.041 0.130 1286 Planarity : 0.004 0.031 1528 Dihedral : 13.994 89.972 3075 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.35 % Allowed : 13.70 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.24), residues: 1064 helix: -0.84 (0.26), residues: 356 sheet: -1.03 (0.48), residues: 137 loop : -1.69 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 122 HIS 0.005 0.001 HIS A 582 PHE 0.016 0.001 PHE A 262 TYR 0.010 0.001 TYR A 484 ARG 0.003 0.000 ARG B 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 4) link_NAG-ASN : angle 2.82125 ( 12) hydrogen bonds : bond 0.26569 ( 276) hydrogen bonds : angle 8.70019 ( 798) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.98744 ( 12) covalent geometry : bond 0.00318 ( 8577) covalent geometry : angle 0.52810 (11706) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 0.1782 time to fit residues: 14.5680 Evaluate side-chains 50 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091205 restraints weight = 11037.302| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.53 r_work: 0.2901 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8587 Z= 0.209 Angle : 0.612 6.740 11730 Z= 0.312 Chirality : 0.044 0.142 1286 Planarity : 0.004 0.033 1528 Dihedral : 4.527 22.976 1250 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.64 % Allowed : 14.17 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.25), residues: 1064 helix: 0.14 (0.28), residues: 371 sheet: -1.12 (0.47), residues: 138 loop : -1.88 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 122 HIS 0.006 0.001 HIS A 500 PHE 0.020 0.002 PHE A 262 TYR 0.018 0.002 TYR B 435 ARG 0.003 0.001 ARG B 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 1.94153 ( 12) hydrogen bonds : bond 0.05076 ( 276) hydrogen bonds : angle 5.56223 ( 798) SS BOND : bond 0.00537 ( 6) SS BOND : angle 1.28812 ( 12) covalent geometry : bond 0.00513 ( 8577) covalent geometry : angle 0.60819 (11706) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.7374 (tmm) cc_final: 0.6402 (tpp) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 0.1573 time to fit residues: 16.7316 Evaluate side-chains 59 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096432 restraints weight = 10966.657| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.49 r_work: 0.2962 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8587 Z= 0.114 Angle : 0.525 6.915 11730 Z= 0.264 Chirality : 0.041 0.137 1286 Planarity : 0.004 0.032 1528 Dihedral : 4.142 19.617 1249 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.34 % Allowed : 15.11 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.25), residues: 1064 helix: 0.82 (0.29), residues: 362 sheet: -1.04 (0.47), residues: 138 loop : -1.77 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 122 HIS 0.004 0.001 HIS A 582 PHE 0.015 0.001 PHE A 262 TYR 0.014 0.001 TYR A 484 ARG 0.001 0.000 ARG B 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 4) link_NAG-ASN : angle 1.48980 ( 12) hydrogen bonds : bond 0.03681 ( 276) hydrogen bonds : angle 4.91488 ( 798) SS BOND : bond 0.00149 ( 6) SS BOND : angle 0.95038 ( 12) covalent geometry : bond 0.00273 ( 8577) covalent geometry : angle 0.52246 (11706) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7916 (t0) cc_final: 0.7533 (t0) REVERT: A 386 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: A 446 MET cc_start: 0.7393 (tmm) cc_final: 0.6283 (tpp) REVERT: B 386 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.7955 (mt-10) outliers start: 20 outliers final: 10 residues processed: 73 average time/residue: 0.1534 time to fit residues: 17.5968 Evaluate side-chains 62 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 31 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 35 optimal weight: 0.0770 chunk 49 optimal weight: 0.0040 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098851 restraints weight = 10731.622| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.36 r_work: 0.3011 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8587 Z= 0.090 Angle : 0.495 6.640 11730 Z= 0.249 Chirality : 0.040 0.127 1286 Planarity : 0.003 0.030 1528 Dihedral : 3.922 19.241 1249 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.11 % Allowed : 15.81 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 1064 helix: 1.18 (0.29), residues: 362 sheet: -0.98 (0.47), residues: 139 loop : -1.68 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 122 HIS 0.004 0.000 HIS A 582 PHE 0.011 0.001 PHE A 262 TYR 0.013 0.001 TYR B 435 ARG 0.001 0.000 ARG B 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 4) link_NAG-ASN : angle 1.34795 ( 12) hydrogen bonds : bond 0.02950 ( 276) hydrogen bonds : angle 4.55250 ( 798) SS BOND : bond 0.00498 ( 6) SS BOND : angle 0.86945 ( 12) covalent geometry : bond 0.00206 ( 8577) covalent geometry : angle 0.49299 (11706) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.7470 (tmm) cc_final: 0.6406 (tpp) REVERT: B 386 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.7939 (mt-10) outliers start: 18 outliers final: 8 residues processed: 72 average time/residue: 0.1520 time to fit residues: 17.2245 Evaluate side-chains 60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 548 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098416 restraints weight = 10695.549| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.38 r_work: 0.3002 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8587 Z= 0.099 Angle : 0.499 7.468 11730 Z= 0.249 Chirality : 0.040 0.127 1286 Planarity : 0.003 0.028 1528 Dihedral : 3.864 19.292 1249 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.87 % Allowed : 16.16 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1064 helix: 1.29 (0.29), residues: 362 sheet: -0.94 (0.46), residues: 139 loop : -1.67 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 122 HIS 0.005 0.001 HIS A 582 PHE 0.013 0.001 PHE A 262 TYR 0.013 0.001 TYR B 435 ARG 0.001 0.000 ARG A 441 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 4) link_NAG-ASN : angle 1.31827 ( 12) hydrogen bonds : bond 0.02967 ( 276) hydrogen bonds : angle 4.42653 ( 798) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.92018 ( 12) covalent geometry : bond 0.00238 ( 8577) covalent geometry : angle 0.49716 (11706) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: A 446 MET cc_start: 0.7455 (tmm) cc_final: 0.6401 (tpp) REVERT: B 386 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8133 (mt-10) outliers start: 16 outliers final: 9 residues processed: 65 average time/residue: 0.1769 time to fit residues: 17.8963 Evaluate side-chains 61 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 529 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098467 restraints weight = 10738.533| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.37 r_work: 0.2996 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8587 Z= 0.102 Angle : 0.502 6.946 11730 Z= 0.250 Chirality : 0.041 0.137 1286 Planarity : 0.003 0.027 1528 Dihedral : 3.841 19.436 1249 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.76 % Allowed : 16.63 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.26), residues: 1064 helix: 1.36 (0.29), residues: 363 sheet: -0.88 (0.46), residues: 138 loop : -1.67 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 122 HIS 0.004 0.001 HIS A 582 PHE 0.013 0.001 PHE A 262 TYR 0.012 0.001 TYR B 435 ARG 0.001 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 4) link_NAG-ASN : angle 1.28103 ( 12) hydrogen bonds : bond 0.02939 ( 276) hydrogen bonds : angle 4.36639 ( 798) SS BOND : bond 0.00199 ( 6) SS BOND : angle 0.92900 ( 12) covalent geometry : bond 0.00246 ( 8577) covalent geometry : angle 0.49998 (11706) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: A 446 MET cc_start: 0.7466 (tmm) cc_final: 0.6442 (tpp) REVERT: B 386 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8088 (mt-10) outliers start: 15 outliers final: 10 residues processed: 62 average time/residue: 0.2508 time to fit residues: 24.6137 Evaluate side-chains 62 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 596 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 81 optimal weight: 0.0070 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098020 restraints weight = 10693.524| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.38 r_work: 0.2998 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8587 Z= 0.107 Angle : 0.507 7.093 11730 Z= 0.253 Chirality : 0.041 0.129 1286 Planarity : 0.003 0.027 1528 Dihedral : 3.826 19.389 1249 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.76 % Allowed : 17.10 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.26), residues: 1064 helix: 1.38 (0.29), residues: 363 sheet: -0.91 (0.46), residues: 139 loop : -1.67 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 122 HIS 0.005 0.001 HIS A 582 PHE 0.013 0.001 PHE A 262 TYR 0.012 0.001 TYR B 435 ARG 0.001 0.000 ARG A 441 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 4) link_NAG-ASN : angle 1.26416 ( 12) hydrogen bonds : bond 0.02950 ( 276) hydrogen bonds : angle 4.33672 ( 798) SS BOND : bond 0.00201 ( 6) SS BOND : angle 0.94236 ( 12) covalent geometry : bond 0.00259 ( 8577) covalent geometry : angle 0.50492 (11706) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: A 446 MET cc_start: 0.7489 (tmm) cc_final: 0.6447 (tpp) REVERT: B 386 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8062 (mt-10) outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.2662 time to fit residues: 25.8168 Evaluate side-chains 61 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 529 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 61 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099025 restraints weight = 10761.938| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.39 r_work: 0.3016 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8587 Z= 0.094 Angle : 0.495 7.153 11730 Z= 0.246 Chirality : 0.041 0.135 1286 Planarity : 0.003 0.027 1528 Dihedral : 3.773 19.204 1249 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.76 % Allowed : 16.98 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.26), residues: 1064 helix: 1.45 (0.29), residues: 363 sheet: -0.85 (0.46), residues: 139 loop : -1.63 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 122 HIS 0.006 0.001 HIS A 582 PHE 0.012 0.001 PHE A 262 TYR 0.013 0.001 TYR A 484 ARG 0.001 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 4) link_NAG-ASN : angle 1.22085 ( 12) hydrogen bonds : bond 0.02758 ( 276) hydrogen bonds : angle 4.26722 ( 798) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.89716 ( 12) covalent geometry : bond 0.00226 ( 8577) covalent geometry : angle 0.49310 (11706) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: A 446 MET cc_start: 0.7466 (tmm) cc_final: 0.6426 (tpp) REVERT: B 386 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8052 (mt-10) outliers start: 15 outliers final: 11 residues processed: 61 average time/residue: 0.1886 time to fit residues: 17.4162 Evaluate side-chains 63 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 596 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097766 restraints weight = 10834.817| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.37 r_work: 0.2997 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8587 Z= 0.115 Angle : 0.514 7.041 11730 Z= 0.256 Chirality : 0.041 0.136 1286 Planarity : 0.003 0.029 1528 Dihedral : 3.828 19.403 1249 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.87 % Allowed : 16.39 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1064 helix: 1.47 (0.29), residues: 362 sheet: -0.88 (0.46), residues: 139 loop : -1.68 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 495 HIS 0.006 0.001 HIS A 582 PHE 0.014 0.001 PHE B 262 TYR 0.014 0.001 TYR A 484 ARG 0.003 0.000 ARG A 594 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 4) link_NAG-ASN : angle 1.24241 ( 12) hydrogen bonds : bond 0.02999 ( 276) hydrogen bonds : angle 4.31512 ( 798) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.97438 ( 12) covalent geometry : bond 0.00281 ( 8577) covalent geometry : angle 0.51244 (11706) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: A 446 MET cc_start: 0.7555 (tmm) cc_final: 0.6470 (tpp) REVERT: B 386 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8031 (mt-10) outliers start: 16 outliers final: 10 residues processed: 61 average time/residue: 0.1522 time to fit residues: 14.9843 Evaluate side-chains 60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 596 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 0.0770 chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096327 restraints weight = 10826.534| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.61 r_work: 0.2967 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8587 Z= 0.131 Angle : 0.527 7.106 11730 Z= 0.263 Chirality : 0.042 0.130 1286 Planarity : 0.003 0.028 1528 Dihedral : 3.933 19.633 1249 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.52 % Allowed : 16.74 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1064 helix: 1.43 (0.29), residues: 362 sheet: -0.95 (0.46), residues: 138 loop : -1.71 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 495 HIS 0.006 0.001 HIS A 582 PHE 0.016 0.001 PHE B 565 TYR 0.015 0.001 TYR A 484 ARG 0.003 0.000 ARG A 594 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 4) link_NAG-ASN : angle 1.24051 ( 12) hydrogen bonds : bond 0.03163 ( 276) hydrogen bonds : angle 4.37025 ( 798) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.02175 ( 12) covalent geometry : bond 0.00326 ( 8577) covalent geometry : angle 0.52500 (11706) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: A 446 MET cc_start: 0.7323 (tmm) cc_final: 0.6344 (tpp) REVERT: B 386 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.7983 (mt-10) outliers start: 13 outliers final: 10 residues processed: 59 average time/residue: 0.1589 time to fit residues: 14.9440 Evaluate side-chains 62 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 596 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097438 restraints weight = 10896.336| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.47 r_work: 0.2983 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8587 Z= 0.108 Angle : 0.511 7.102 11730 Z= 0.255 Chirality : 0.041 0.145 1286 Planarity : 0.003 0.027 1528 Dihedral : 3.868 19.375 1249 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.64 % Allowed : 16.86 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.26), residues: 1064 helix: 1.50 (0.29), residues: 362 sheet: -0.93 (0.46), residues: 139 loop : -1.68 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 122 HIS 0.006 0.001 HIS A 582 PHE 0.014 0.001 PHE B 565 TYR 0.014 0.001 TYR A 484 ARG 0.002 0.000 ARG A 594 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 4) link_NAG-ASN : angle 1.20085 ( 12) hydrogen bonds : bond 0.02930 ( 276) hydrogen bonds : angle 4.34153 ( 798) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.93713 ( 12) covalent geometry : bond 0.00264 ( 8577) covalent geometry : angle 0.50931 (11706) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4496.71 seconds wall clock time: 80 minutes 36.02 seconds (4836.02 seconds total)