Starting phenix.real_space_refine on Fri Aug 22 22:37:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7d_29811/08_2025/8g7d_29811.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7d_29811/08_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_29811/08_2025/8g7d_29811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7d_29811/08_2025/8g7d_29811.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7d_29811/08_2025/8g7d_29811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7d_29811/08_2025/8g7d_29811.cif" } resolution = 3.28 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= 0.005 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): 0.00s 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: 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: {'ASN:plan1': 2, 'GLU:plan': 10, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} 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: {'ASN:plan1': 1, 'GLN:plan1': 2, 'GLU:plan': 8, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 1} 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: 1.43, per 1000 atoms: 0.17 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: 0.45 Conformation dependent library (CDL) restraints added in 350.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.25 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: 1.25 Time building geometry restraints manager: 0.63 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 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.110 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- 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 : 6.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (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 ARG 0.003 0.000 ARG B 97 TYR 0.010 0.001 TYR A 484 PHE 0.016 0.001 PHE A 262 TRP 0.007 0.001 TRP B 122 HIS 0.005 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8577) covalent geometry : angle 0.52810 (11706) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.98744 ( 12) hydrogen bonds : bond 0.26569 ( 276) hydrogen bonds : angle 8.70019 ( 798) link_NAG-ASN : bond 0.00485 ( 4) link_NAG-ASN : angle 2.82125 ( 12) *********************** 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 : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 0.0659 time to fit residues: 5.4300 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 : 0.279 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.126910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094881 restraints weight = 10953.442| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.69 r_work: 0.2957 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8587 Z= 0.146 Angle : 0.563 6.300 11730 Z= 0.287 Chirality : 0.042 0.134 1286 Planarity : 0.004 0.031 1528 Dihedral : 4.322 22.497 1250 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.41 % Allowed : 13.82 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.25), residues: 1064 helix: 0.35 (0.28), residues: 366 sheet: -1.01 (0.48), residues: 138 loop : -1.80 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 492 TYR 0.016 0.001 TYR B 435 PHE 0.016 0.001 PHE A 262 TRP 0.010 0.001 TRP B 122 HIS 0.005 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8577) covalent geometry : angle 0.55912 (11706) SS BOND : bond 0.00337 ( 6) SS BOND : angle 1.11608 ( 12) hydrogen bonds : bond 0.04606 ( 276) hydrogen bonds : angle 5.48417 ( 798) link_NAG-ASN : bond 0.00391 ( 4) link_NAG-ASN : angle 1.83553 ( 12) *********************** 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 68 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.7237 (tmm) cc_final: 0.6255 (tpp) outliers start: 12 outliers final: 5 residues processed: 67 average time/residue: 0.0672 time to fit residues: 7.1318 Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 26 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 57 optimal weight: 0.0060 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098819 restraints weight = 10714.240| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.37 r_work: 0.3003 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8587 Z= 0.094 Angle : 0.501 7.159 11730 Z= 0.251 Chirality : 0.040 0.128 1286 Planarity : 0.004 0.032 1528 Dihedral : 3.952 18.023 1249 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.87 % Allowed : 13.93 % 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 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: -0.94 (0.26), residues: 1064 helix: 0.95 (0.29), residues: 363 sheet: -0.91 (0.48), residues: 138 loop : -1.67 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 441 TYR 0.014 0.001 TYR A 484 PHE 0.011 0.001 PHE A 262 TRP 0.011 0.001 TRP B 122 HIS 0.003 0.000 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8577) covalent geometry : angle 0.49889 (11706) SS BOND : bond 0.00182 ( 6) SS BOND : angle 0.85239 ( 12) hydrogen bonds : bond 0.03339 ( 276) hydrogen bonds : angle 4.76761 ( 798) link_NAG-ASN : bond 0.00392 ( 4) link_NAG-ASN : angle 1.38531 ( 12) *********************** 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 75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7921 (t0) cc_final: 0.7670 (t0) REVERT: A 386 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: A 446 MET cc_start: 0.7417 (tmm) cc_final: 0.6304 (tpp) REVERT: B 386 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.7699 (mt-10) outliers start: 16 outliers final: 5 residues processed: 73 average time/residue: 0.0655 time to fit residues: 7.5523 Evaluate side-chains 59 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 CYS 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 386 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.0020 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.128075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096949 restraints weight = 10932.635| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.48 r_work: 0.2970 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8587 Z= 0.128 Angle : 0.520 6.723 11730 Z= 0.261 Chirality : 0.042 0.131 1286 Planarity : 0.004 0.028 1528 Dihedral : 3.986 19.276 1249 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % 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 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: -0.91 (0.26), residues: 1064 helix: 1.07 (0.29), residues: 363 sheet: -0.95 (0.47), residues: 138 loop : -1.69 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.014 0.001 TYR B 435 PHE 0.016 0.001 PHE B 262 TRP 0.008 0.001 TRP B 122 HIS 0.005 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8577) covalent geometry : angle 0.51723 (11706) SS BOND : bond 0.00270 ( 6) SS BOND : angle 1.01146 ( 12) hydrogen bonds : bond 0.03404 ( 276) hydrogen bonds : angle 4.63875 ( 798) link_NAG-ASN : bond 0.00374 ( 4) link_NAG-ASN : angle 1.38916 ( 12) *********************** 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 74 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7949 (t0) cc_final: 0.7650 (t0) REVERT: A 446 MET cc_start: 0.7416 (tmm) cc_final: 0.6342 (tpp) REVERT: B 386 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8155 (mt-10) outliers start: 20 outliers final: 10 residues processed: 70 average time/residue: 0.0644 time to fit residues: 7.1583 Evaluate side-chains 63 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 513 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.128905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097944 restraints weight = 10806.926| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.39 r_work: 0.2995 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8587 Z= 0.107 Angle : 0.503 6.812 11730 Z= 0.252 Chirality : 0.041 0.126 1286 Planarity : 0.003 0.027 1528 Dihedral : 3.920 19.199 1249 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.76 % Allowed : 15.57 % Favored : 82.67 % 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: -0.80 (0.26), residues: 1064 helix: 1.22 (0.29), residues: 363 sheet: -0.92 (0.47), residues: 138 loop : -1.67 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 441 TYR 0.014 0.001 TYR B 435 PHE 0.014 0.001 PHE A 262 TRP 0.008 0.001 TRP B 122 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8577) covalent geometry : angle 0.50038 (11706) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.94784 ( 12) hydrogen bonds : bond 0.03077 ( 276) hydrogen bonds : angle 4.48844 ( 798) link_NAG-ASN : bond 0.00371 ( 4) link_NAG-ASN : angle 1.31753 ( 12) *********************** 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: 15 poor density : 53 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7882 (t0) cc_final: 0.7655 (t0) REVERT: A 386 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: A 446 MET cc_start: 0.7453 (tmm) cc_final: 0.6406 (tpp) REVERT: B 386 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8129 (mt-10) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.0682 time to fit residues: 6.8836 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 : 0.286 ------------------------------------------------------------------------------- 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 434 MET 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 30 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.125353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094276 restraints weight = 10964.849| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.48 r_work: 0.2955 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8587 Z= 0.189 Angle : 0.566 7.267 11730 Z= 0.285 Chirality : 0.043 0.138 1286 Planarity : 0.004 0.028 1528 Dihedral : 4.169 20.379 1249 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.11 % Allowed : 16.51 % Favored : 81.38 % 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: -0.98 (0.25), residues: 1064 helix: 1.06 (0.28), residues: 363 sheet: -1.04 (0.46), residues: 138 loop : -1.77 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 441 TYR 0.015 0.002 TYR B 435 PHE 0.019 0.002 PHE A 262 TRP 0.006 0.001 TRP A 601 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8577) covalent geometry : angle 0.56336 (11706) SS BOND : bond 0.00306 ( 6) SS BOND : angle 1.17129 ( 12) hydrogen bonds : bond 0.03789 ( 276) hydrogen bonds : angle 4.63292 ( 798) link_NAG-ASN : bond 0.00366 ( 4) link_NAG-ASN : angle 1.41213 ( 12) *********************** 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 66 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.8020 (t0) cc_final: 0.7779 (t0) REVERT: A 386 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: A 446 MET cc_start: 0.7473 (tmm) cc_final: 0.6465 (tpp) REVERT: B 386 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.7539 (mt-10) outliers start: 18 outliers final: 10 residues processed: 61 average time/residue: 0.0746 time to fit residues: 7.1804 Evaluate side-chains 59 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 A residue 470 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 98 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.128957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098111 restraints weight = 10832.937| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.38 r_work: 0.2999 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1356 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= 0.095 Angle : 0.503 6.912 11730 Z= 0.250 Chirality : 0.040 0.130 1286 Planarity : 0.003 0.028 1528 Dihedral : 3.941 19.371 1249 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.52 % Allowed : 16.63 % Favored : 81.85 % 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: -0.79 (0.26), residues: 1064 helix: 1.27 (0.29), residues: 364 sheet: -1.00 (0.46), residues: 139 loop : -1.68 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 335 TYR 0.013 0.001 TYR A 484 PHE 0.012 0.001 PHE A 262 TRP 0.010 0.001 TRP B 122 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8577) covalent geometry : angle 0.50072 (11706) SS BOND : bond 0.00166 ( 6) SS BOND : angle 0.89995 ( 12) hydrogen bonds : bond 0.02960 ( 276) hydrogen bonds : angle 4.42835 ( 798) link_NAG-ASN : bond 0.00362 ( 4) link_NAG-ASN : angle 1.27849 ( 12) *********************** 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 66 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7860 (t0) cc_final: 0.7609 (t0) REVERT: A 386 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: A 446 MET cc_start: 0.7457 (tmm) cc_final: 0.6404 (tpp) REVERT: B 368 MET cc_start: 0.8691 (mtm) cc_final: 0.8331 (mtt) REVERT: B 386 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8073 (mt-10) outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 0.0710 time to fit residues: 6.8603 Evaluate side-chains 62 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 106 optimal weight: 0.0270 chunk 22 optimal weight: 3.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.125432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094346 restraints weight = 10951.238| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.49 r_work: 0.2959 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8587 Z= 0.177 Angle : 0.570 7.289 11730 Z= 0.285 Chirality : 0.043 0.136 1286 Planarity : 0.004 0.028 1528 Dihedral : 4.157 20.228 1249 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.76 % Allowed : 16.74 % 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 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: -0.96 (0.25), residues: 1064 helix: 1.12 (0.29), residues: 363 sheet: -1.08 (0.46), residues: 138 loop : -1.78 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.016 0.002 TYR B 435 PHE 0.019 0.002 PHE A 262 TRP 0.005 0.001 TRP A 298 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8577) covalent geometry : angle 0.56745 (11706) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.14734 ( 12) hydrogen bonds : bond 0.03662 ( 276) hydrogen bonds : angle 4.56735 ( 798) link_NAG-ASN : bond 0.00341 ( 4) link_NAG-ASN : angle 1.36822 ( 12) *********************** 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 63 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7930 (t0) cc_final: 0.7659 (t0) REVERT: A 386 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: A 446 MET cc_start: 0.7460 (tmm) cc_final: 0.6452 (tpp) REVERT: B 386 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: B 445 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7757 (tt0) outliers start: 15 outliers final: 11 residues processed: 59 average time/residue: 0.0673 time to fit residues: 6.1417 Evaluate side-chains 60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 A residue 513 VAL 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 529 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.127640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096786 restraints weight = 10781.679| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.38 r_work: 0.2977 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8587 Z= 0.120 Angle : 0.530 6.885 11730 Z= 0.265 Chirality : 0.042 0.140 1286 Planarity : 0.003 0.028 1528 Dihedral : 4.056 19.889 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 : 1.99 % Allowed : 16.74 % 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 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: -0.86 (0.26), residues: 1064 helix: 1.25 (0.29), residues: 363 sheet: -1.07 (0.45), residues: 139 loop : -1.74 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 441 TYR 0.015 0.001 TYR A 484 PHE 0.014 0.001 PHE A 262 TRP 0.009 0.001 TRP B 122 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8577) covalent geometry : angle 0.52779 (11706) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.99310 ( 12) hydrogen bonds : bond 0.03164 ( 276) hydrogen bonds : angle 4.47664 ( 798) link_NAG-ASN : bond 0.00338 ( 4) link_NAG-ASN : angle 1.27042 ( 12) *********************** 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 68 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7892 (t0) cc_final: 0.7659 (t0) REVERT: A 386 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: A 446 MET cc_start: 0.7551 (tmm) cc_final: 0.6446 (tpp) REVERT: B 368 MET cc_start: 0.8774 (mtm) cc_final: 0.8462 (mtt) REVERT: B 445 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7744 (tt0) outliers start: 17 outliers final: 11 residues processed: 64 average time/residue: 0.0755 time to fit residues: 7.5607 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 : 0.323 ------------------------------------------------------------------------------- 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 A residue 470 LEU Chi-restraints excluded: chain A residue 513 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 31 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 chunk 45 optimal weight: 0.0170 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.129107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097155 restraints weight = 10697.784| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.56 r_work: 0.2982 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8587 Z= 0.098 Angle : 0.511 7.013 11730 Z= 0.253 Chirality : 0.041 0.140 1286 Planarity : 0.003 0.030 1528 Dihedral : 3.890 19.123 1249 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.17 % Allowed : 17.45 % Favored : 81.38 % 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: -0.71 (0.26), residues: 1064 helix: 1.38 (0.29), residues: 364 sheet: -0.91 (0.46), residues: 140 loop : -1.68 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 82 TYR 0.013 0.001 TYR A 484 PHE 0.013 0.001 PHE A 262 TRP 0.010 0.001 TRP B 122 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8577) covalent geometry : angle 0.50951 (11706) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.87215 ( 12) hydrogen bonds : bond 0.02865 ( 276) hydrogen bonds : angle 4.35487 ( 798) link_NAG-ASN : bond 0.00339 ( 4) link_NAG-ASN : angle 1.23967 ( 12) ********************** 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 60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: A 446 MET cc_start: 0.7334 (tmm) cc_final: 0.6336 (tpp) REVERT: B 368 MET cc_start: 0.8703 (mtm) cc_final: 0.8405 (mtt) REVERT: B 386 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.7953 (mt-10) outliers start: 10 outliers final: 8 residues processed: 58 average time/residue: 0.0759 time to fit residues: 7.0572 Evaluate side-chains 61 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 A residue 513 VAL 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 426 VAL Chi-restraints excluded: chain B residue 529 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.127470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096126 restraints weight = 10708.955| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.45 r_work: 0.2965 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8587 Z= 0.141 Angle : 0.553 10.025 11730 Z= 0.274 Chirality : 0.043 0.162 1286 Planarity : 0.004 0.028 1528 Dihedral : 4.005 19.681 1249 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.64 % Allowed : 17.21 % 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 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: -0.82 (0.26), residues: 1064 helix: 1.30 (0.29), residues: 363 sheet: -1.03 (0.46), residues: 139 loop : -1.72 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.015 0.001 TYR B 435 PHE 0.020 0.001 PHE A 565 TRP 0.006 0.001 TRP B 122 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8577) covalent geometry : angle 0.55127 (11706) SS BOND : bond 0.00224 ( 6) SS BOND : angle 1.04128 ( 12) hydrogen bonds : bond 0.03274 ( 276) hydrogen bonds : angle 4.45807 ( 798) link_NAG-ASN : bond 0.00333 ( 4) link_NAG-ASN : angle 1.26827 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.38 seconds wall clock time: 33 minutes 35.72 seconds (2015.72 seconds total)