Starting phenix.real_space_refine on Sat Aug 23 12:52:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzd_41755/08_2025/8tzd_41755_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzd_41755/08_2025/8tzd_41755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzd_41755/08_2025/8tzd_41755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzd_41755/08_2025/8tzd_41755.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzd_41755/08_2025/8tzd_41755_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzd_41755/08_2025/8tzd_41755_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 85 5.16 5 C 8073 2.51 5 N 1908 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12175 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3971 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.52, per 1000 atoms: 0.29 Number of scatterers: 12175 At special positions: 0 Unit cell: (129.6, 127.44, 79.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 1 15.00 O 2108 8.00 N 1908 7.00 C 8073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 704.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 130 through 157 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 157 through 198 Proline residue: A 167 - end of helix removed outlier: 5.021A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.574A pdb=" N VAL A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.309A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 281 removed outlier: 3.539A pdb=" N PHE A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 312 removed outlier: 4.539A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.603A pdb=" N TRP A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.668A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 removed outlier: 3.555A pdb=" N ARG A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.180A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 437 through 481 removed outlier: 3.963A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 496 through 504 removed outlier: 3.562A pdb=" N GLY A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.758A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 586 Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 596 through 619 Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.678A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 4.022A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 4.547A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 271 Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.768A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 312 removed outlier: 4.292A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.799A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.865A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.712A pdb=" N LEU B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 480 removed outlier: 3.665A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.598A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.700A pdb=" N GLY B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 524 through 542 removed outlier: 4.078A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 589 through 596 removed outlier: 3.650A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 619 removed outlier: 3.621A pdb=" N LEU B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 602 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 130 through 157 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 157 through 203 Proline residue: C 167 - end of helix removed outlier: 4.405A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.825A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 removed outlier: 3.522A pdb=" N PHE C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 277 removed outlier: 4.015A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 312 removed outlier: 4.322A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 312 through 329 removed outlier: 3.697A pdb=" N TRP C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 341 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 379 through 389 removed outlier: 4.311A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 389 " --> pdb=" O TYR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.217A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 480 removed outlier: 4.138A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 removed outlier: 4.521A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 509 through 523 removed outlier: 3.550A pdb=" N VAL C 513 " --> pdb=" O ASP C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.891A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 573 through 586 removed outlier: 4.410A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 596 removed outlier: 3.673A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 618 removed outlier: 3.525A pdb=" N ALA C 600 " --> pdb=" O GLY C 596 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2892 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: 2.04 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1821 1.29 - 1.42: 3476 1.42 - 1.55: 7045 1.55 - 1.68: 14 1.68 - 1.81: 153 Bond restraints: 12509 Sorted by residual: bond pdb=" C11 XMO A 701 " pdb=" O12 XMO A 701 " ideal model delta sigma weight residual 1.398 1.680 -0.282 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C11 XMO C 701 " pdb=" O12 XMO C 701 " ideal model delta sigma weight residual 1.398 1.678 -0.280 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C11 XMO B 701 " pdb=" O12 XMO B 701 " ideal model delta sigma weight residual 1.398 1.677 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C10 XMO A 701 " pdb=" C11 XMO A 701 " ideal model delta sigma weight residual 1.534 1.289 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C10 XMO C 701 " pdb=" C11 XMO C 701 " ideal model delta sigma weight residual 1.534 1.289 0.245 2.00e-02 2.50e+03 1.50e+02 ... (remaining 12504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 16954 3.22 - 6.43: 76 6.43 - 9.65: 7 9.65 - 12.87: 1 12.87 - 16.09: 1 Bond angle restraints: 17039 Sorted by residual: angle pdb=" O1 LBN A 702 " pdb=" P1 LBN A 702 " pdb=" O2 LBN A 702 " ideal model delta sigma weight residual 93.45 109.54 -16.09 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O3 LBN A 702 " pdb=" P1 LBN A 702 " pdb=" O4 LBN A 702 " ideal model delta sigma weight residual 119.36 109.58 9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C26 LBN A 702 " pdb=" C25 LBN A 702 " pdb=" O5 LBN A 702 " ideal model delta sigma weight residual 111.43 120.73 -9.30 3.00e+00 1.11e-01 9.62e+00 angle pdb=" C02 XMO B 701 " pdb=" C04 XMO B 701 " pdb=" O06 XMO B 701 " ideal model delta sigma weight residual 111.45 120.37 -8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" C35 LBN A 702 " pdb=" C34 LBN A 702 " pdb=" O7 LBN A 702 " ideal model delta sigma weight residual 111.21 119.63 -8.42 3.00e+00 1.11e-01 7.88e+00 ... (remaining 17034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 7067 33.74 - 67.48: 104 67.48 - 101.22: 13 101.22 - 134.96: 2 134.96 - 168.70: 4 Dihedral angle restraints: 7190 sinusoidal: 2632 harmonic: 4558 Sorted by residual: dihedral pdb=" C01 XMO C 701 " pdb=" C02 XMO C 701 " pdb=" C04 XMO C 701 " pdb=" O06 XMO C 701 " ideal model delta sinusoidal sigma weight residual 296.92 128.22 168.70 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C01 XMO C 701 " pdb=" C02 XMO C 701 " pdb=" C04 XMO C 701 " pdb=" O05 XMO C 701 " ideal model delta sinusoidal sigma weight residual 116.78 -51.39 168.17 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C01 XMO B 701 " pdb=" C02 XMO B 701 " pdb=" C04 XMO B 701 " pdb=" O06 XMO B 701 " ideal model delta sinusoidal sigma weight residual 296.92 145.76 151.16 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 7187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1826 0.070 - 0.141: 144 0.141 - 0.211: 1 0.211 - 0.282: 0 0.282 - 0.352: 3 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C10 XMO B 701 " pdb=" C09 XMO B 701 " pdb=" C11 XMO B 701 " pdb=" O22 XMO B 701 " both_signs ideal model delta sigma weight residual False 2.74 2.39 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C10 XMO C 701 " pdb=" C09 XMO C 701 " pdb=" C11 XMO C 701 " pdb=" O22 XMO C 701 " both_signs ideal model delta sigma weight residual False 2.74 2.39 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C10 XMO A 701 " pdb=" C09 XMO A 701 " pdb=" C11 XMO A 701 " pdb=" O22 XMO A 701 " both_signs ideal model delta sigma weight residual False 2.74 2.39 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 1971 not shown) Planarity restraints: 2069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 233 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 234 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 233 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO C 234 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 403 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 404 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " 0.033 5.00e-02 4.00e+02 ... (remaining 2066 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 659 2.73 - 3.27: 12959 3.27 - 3.81: 20610 3.81 - 4.36: 22805 4.36 - 4.90: 41485 Nonbonded interactions: 98518 Sorted by model distance: nonbonded pdb=" OG SER B 380 " pdb=" O21 XMO B 701 " model vdw 2.183 3.040 nonbonded pdb=" O LEU B 195 " pdb=" OG1 THR B 199 " model vdw 2.203 3.040 nonbonded pdb=" O LEU A 248 " pdb=" OG1 THR A 252 " model vdw 2.227 3.040 nonbonded pdb=" O ALA A 275 " pdb=" OG SER A 278 " model vdw 2.266 3.040 nonbonded pdb=" OG SER C 574 " pdb=" O22 XMO C 701 " model vdw 2.322 3.040 ... (remaining 98513 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 90 through 701) selection = (chain 'B' and (resid 90 through 421 or resid 434 through 701)) selection = (chain 'C' and (resid 90 through 421 or resid 434 through 701)) } 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: 1.510 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.370 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.009 0.282 12509 Z= 0.467 Angle : 0.580 16.085 17039 Z= 0.293 Chirality : 0.039 0.352 1974 Planarity : 0.004 0.064 2069 Dihedral : 13.903 168.704 4266 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.32 % Allowed : 1.37 % Favored : 98.31 % 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: 2.98 (0.21), residues: 1579 helix: 2.47 (0.15), residues: 1291 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.008 0.001 TYR B 231 PHE 0.017 0.001 PHE B 413 TRP 0.012 0.001 TRP C 316 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00950 (12509) covalent geometry : angle 0.58014 (17039) hydrogen bonds : bond 0.13349 ( 978) hydrogen bonds : angle 5.10205 ( 2892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 220 time to evaluate : 0.444 Fit side-chains REVERT: A 284 LYS cc_start: 0.8586 (mttm) cc_final: 0.8025 (mmtt) REVERT: A 307 MET cc_start: 0.8627 (mtp) cc_final: 0.8411 (mtp) REVERT: A 470 MET cc_start: 0.8183 (mmt) cc_final: 0.7782 (mmt) REVERT: A 564 TYR cc_start: 0.8569 (m-80) cc_final: 0.8171 (m-80) REVERT: B 154 MET cc_start: 0.6859 (tpt) cc_final: 0.6308 (tpt) REVERT: B 195 LEU cc_start: 0.7310 (tt) cc_final: 0.7105 (tp) REVERT: B 305 MET cc_start: 0.7951 (mmt) cc_final: 0.7665 (mmp) REVERT: B 355 ARG cc_start: 0.8011 (tmm-80) cc_final: 0.7598 (ttm170) REVERT: B 357 TYR cc_start: 0.7682 (m-80) cc_final: 0.7481 (m-80) REVERT: C 252 THR cc_start: 0.8490 (m) cc_final: 0.8171 (p) REVERT: C 423 ASN cc_start: 0.7887 (t0) cc_final: 0.7678 (t0) REVERT: C 502 MET cc_start: 0.7559 (mmp) cc_final: 0.6769 (mtp) REVERT: C 562 SER cc_start: 0.9009 (t) cc_final: 0.8619 (m) outliers start: 4 outliers final: 3 residues processed: 224 average time/residue: 0.1004 time to fit residues: 33.9337 Evaluate side-chains 180 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 177 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 571 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN B 444 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127058 restraints weight = 14013.626| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.10 r_work: 0.3055 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12509 Z= 0.159 Angle : 0.510 6.785 17039 Z= 0.269 Chirality : 0.038 0.152 1974 Planarity : 0.004 0.051 2069 Dihedral : 10.568 168.114 1780 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.45 % Allowed : 7.50 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.21), residues: 1579 helix: 2.55 (0.14), residues: 1315 sheet: None (None), residues: 0 loop : -0.59 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.012 0.001 TYR A 385 PHE 0.017 0.001 PHE B 413 TRP 0.011 0.001 TRP B 316 HIS 0.003 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00346 (12509) covalent geometry : angle 0.50974 (17039) hydrogen bonds : bond 0.06032 ( 978) hydrogen bonds : angle 4.02606 ( 2892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.498 Fit side-chains REVERT: A 284 LYS cc_start: 0.8580 (mttm) cc_final: 0.8201 (mmtt) REVERT: B 154 MET cc_start: 0.7423 (tpt) cc_final: 0.6864 (tpt) REVERT: B 305 MET cc_start: 0.7863 (mmt) cc_final: 0.7658 (mmp) REVERT: B 314 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8314 (ptm) REVERT: B 355 ARG cc_start: 0.8481 (tmm-80) cc_final: 0.8106 (ttm170) REVERT: B 357 TYR cc_start: 0.8008 (m-80) cc_final: 0.7740 (m-80) REVERT: B 482 ASP cc_start: 0.8949 (t0) cc_final: 0.8705 (t0) REVERT: C 154 MET cc_start: 0.6720 (mmp) cc_final: 0.6287 (mmp) REVERT: C 502 MET cc_start: 0.7609 (mmp) cc_final: 0.7164 (mtp) REVERT: C 562 SER cc_start: 0.8771 (t) cc_final: 0.8533 (m) outliers start: 18 outliers final: 13 residues processed: 190 average time/residue: 0.0916 time to fit residues: 27.0568 Evaluate side-chains 177 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN C 551 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130726 restraints weight = 14077.033| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.33 r_work: 0.3108 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12509 Z= 0.127 Angle : 0.462 8.315 17039 Z= 0.239 Chirality : 0.037 0.145 1974 Planarity : 0.004 0.045 2069 Dihedral : 8.763 131.889 1779 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.53 % Allowed : 9.35 % Favored : 89.11 % 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: 3.32 (0.21), residues: 1579 helix: 2.70 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.61 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.007 0.001 TYR A 385 PHE 0.021 0.001 PHE A 146 TRP 0.010 0.001 TRP B 316 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00262 (12509) covalent geometry : angle 0.46221 (17039) hydrogen bonds : bond 0.05116 ( 978) hydrogen bonds : angle 3.77319 ( 2892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.450 Fit side-chains REVERT: A 154 MET cc_start: 0.6960 (tpp) cc_final: 0.6726 (tpp) REVERT: A 284 LYS cc_start: 0.8589 (mttm) cc_final: 0.8136 (mmtt) REVERT: B 248 LEU cc_start: 0.8454 (tp) cc_final: 0.7985 (mp) REVERT: B 355 ARG cc_start: 0.8456 (tmm-80) cc_final: 0.7899 (ttm170) REVERT: B 357 TYR cc_start: 0.7928 (m-80) cc_final: 0.7638 (m-80) REVERT: B 360 TYR cc_start: 0.8128 (m-10) cc_final: 0.7918 (m-80) REVERT: B 477 LEU cc_start: 0.8115 (tt) cc_final: 0.7274 (tp) REVERT: C 154 MET cc_start: 0.6782 (mmp) cc_final: 0.6221 (mmp) REVERT: C 502 MET cc_start: 0.7550 (mmp) cc_final: 0.7024 (mtp) REVERT: C 562 SER cc_start: 0.8844 (t) cc_final: 0.8575 (m) outliers start: 19 outliers final: 11 residues processed: 184 average time/residue: 0.0994 time to fit residues: 28.0698 Evaluate side-chains 175 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN C 551 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.159838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130572 restraints weight = 14123.164| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.34 r_work: 0.3080 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12509 Z= 0.136 Angle : 0.471 8.169 17039 Z= 0.245 Chirality : 0.037 0.147 1974 Planarity : 0.004 0.045 2069 Dihedral : 8.150 113.265 1776 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.45 % Allowed : 10.00 % Favored : 88.55 % 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: 3.29 (0.21), residues: 1579 helix: 2.69 (0.14), residues: 1319 sheet: None (None), residues: 0 loop : -0.69 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 133 TYR 0.007 0.001 TYR A 385 PHE 0.016 0.001 PHE C 146 TRP 0.010 0.001 TRP B 316 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00294 (12509) covalent geometry : angle 0.47121 (17039) hydrogen bonds : bond 0.05274 ( 978) hydrogen bonds : angle 3.77384 ( 2892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.459 Fit side-chains REVERT: A 133 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7643 (ttp80) REVERT: A 284 LYS cc_start: 0.8611 (mttm) cc_final: 0.8214 (mmtt) REVERT: A 564 TYR cc_start: 0.8298 (m-80) cc_final: 0.8097 (m-80) REVERT: B 248 LEU cc_start: 0.8444 (tp) cc_final: 0.8052 (mp) REVERT: B 355 ARG cc_start: 0.8505 (tmm-80) cc_final: 0.8033 (ttm170) REVERT: B 357 TYR cc_start: 0.8013 (m-80) cc_final: 0.7684 (m-80) REVERT: B 360 TYR cc_start: 0.8139 (m-10) cc_final: 0.7934 (m-80) REVERT: B 584 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8401 (p) REVERT: C 154 MET cc_start: 0.6824 (mmp) cc_final: 0.6324 (mmp) REVERT: C 502 MET cc_start: 0.7640 (mmp) cc_final: 0.7167 (mtp) REVERT: C 562 SER cc_start: 0.8753 (t) cc_final: 0.8536 (m) outliers start: 18 outliers final: 14 residues processed: 178 average time/residue: 0.1015 time to fit residues: 27.7010 Evaluate side-chains 176 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 66 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 571 ASN C 267 GLN C 423 ASN C 551 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.160276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130350 restraints weight = 14099.043| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.13 r_work: 0.3112 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12509 Z= 0.119 Angle : 0.448 8.913 17039 Z= 0.231 Chirality : 0.036 0.140 1974 Planarity : 0.004 0.045 2069 Dihedral : 7.691 100.893 1776 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.85 % Allowed : 10.48 % Favored : 87.66 % 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: 3.43 (0.21), residues: 1579 helix: 2.78 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.66 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.006 0.001 TYR A 385 PHE 0.018 0.001 PHE B 546 TRP 0.014 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00245 (12509) covalent geometry : angle 0.44818 (17039) hydrogen bonds : bond 0.04703 ( 978) hydrogen bonds : angle 3.62793 ( 2892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.494 Fit side-chains REVERT: A 133 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7635 (ttp80) REVERT: A 284 LYS cc_start: 0.8604 (mttm) cc_final: 0.8205 (mmtt) REVERT: A 564 TYR cc_start: 0.8242 (m-80) cc_final: 0.8005 (m-80) REVERT: B 248 LEU cc_start: 0.8261 (tp) cc_final: 0.7961 (mp) REVERT: B 355 ARG cc_start: 0.8409 (tmm-80) cc_final: 0.7967 (ttm170) REVERT: B 357 TYR cc_start: 0.7973 (m-80) cc_final: 0.7614 (m-80) REVERT: B 477 LEU cc_start: 0.8029 (tt) cc_final: 0.7181 (tp) REVERT: B 482 ASP cc_start: 0.8766 (t0) cc_final: 0.8364 (t0) REVERT: C 122 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7259 (mp) REVERT: C 154 MET cc_start: 0.6955 (mmp) cc_final: 0.6513 (mmp) REVERT: C 305 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8144 (mmp) REVERT: C 325 MET cc_start: 0.7833 (mtm) cc_final: 0.7607 (mtm) REVERT: C 502 MET cc_start: 0.7582 (mmp) cc_final: 0.7091 (mtp) outliers start: 23 outliers final: 14 residues processed: 180 average time/residue: 0.0961 time to fit residues: 26.5820 Evaluate side-chains 175 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 413 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN C 551 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.156752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127323 restraints weight = 14155.725| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.36 r_work: 0.3037 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12509 Z= 0.157 Angle : 0.493 8.692 17039 Z= 0.257 Chirality : 0.038 0.155 1974 Planarity : 0.004 0.045 2069 Dihedral : 7.894 105.058 1776 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.61 % Allowed : 10.89 % Favored : 87.50 % 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: 3.13 (0.21), residues: 1579 helix: 2.60 (0.14), residues: 1318 sheet: None (None), residues: 0 loop : -0.82 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.007 0.001 TYR A 385 PHE 0.018 0.001 PHE B 546 TRP 0.016 0.001 TRP B 178 HIS 0.003 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00357 (12509) covalent geometry : angle 0.49252 (17039) hydrogen bonds : bond 0.05825 ( 978) hydrogen bonds : angle 3.85354 ( 2892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.485 Fit side-chains REVERT: A 133 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7713 (ttp80) REVERT: A 154 MET cc_start: 0.7185 (tpp) cc_final: 0.6839 (tpp) REVERT: A 284 LYS cc_start: 0.8544 (mttm) cc_final: 0.8171 (mmtt) REVERT: B 248 LEU cc_start: 0.8308 (tp) cc_final: 0.7967 (mp) REVERT: B 355 ARG cc_start: 0.8485 (tmm-80) cc_final: 0.8134 (ttm170) REVERT: B 357 TYR cc_start: 0.8073 (m-80) cc_final: 0.7645 (m-80) REVERT: B 482 ASP cc_start: 0.8808 (t0) cc_final: 0.8535 (t0) REVERT: C 154 MET cc_start: 0.7018 (mmp) cc_final: 0.6604 (mmp) REVERT: C 502 MET cc_start: 0.7589 (mmp) cc_final: 0.7043 (mtp) outliers start: 20 outliers final: 17 residues processed: 172 average time/residue: 0.0985 time to fit residues: 26.0670 Evaluate side-chains 174 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 35 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 7 optimal weight: 0.0770 chunk 143 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 150 optimal weight: 0.0170 chunk 46 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.135028 restraints weight = 14031.904| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.07 r_work: 0.3121 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12509 Z= 0.112 Angle : 0.444 8.676 17039 Z= 0.227 Chirality : 0.036 0.138 1974 Planarity : 0.004 0.045 2069 Dihedral : 7.417 100.305 1776 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.69 % Allowed : 11.29 % Favored : 87.02 % 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: 3.48 (0.22), residues: 1579 helix: 2.84 (0.14), residues: 1318 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.006 0.001 TYR A 564 PHE 0.027 0.001 PHE A 146 TRP 0.014 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00220 (12509) covalent geometry : angle 0.44431 (17039) hydrogen bonds : bond 0.04499 ( 978) hydrogen bonds : angle 3.58241 ( 2892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.455 Fit side-chains REVERT: A 284 LYS cc_start: 0.8560 (mttm) cc_final: 0.8178 (mmtt) REVERT: B 248 LEU cc_start: 0.8227 (tp) cc_final: 0.7961 (mp) REVERT: B 355 ARG cc_start: 0.8390 (tmm-80) cc_final: 0.8037 (ttm170) REVERT: B 357 TYR cc_start: 0.8008 (m-80) cc_final: 0.7583 (m-80) REVERT: B 477 LEU cc_start: 0.8119 (tt) cc_final: 0.7469 (tt) REVERT: C 154 MET cc_start: 0.6977 (mmp) cc_final: 0.6563 (mmp) REVERT: C 305 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8132 (mmp) REVERT: C 325 MET cc_start: 0.7870 (mtm) cc_final: 0.7615 (mtm) outliers start: 21 outliers final: 15 residues processed: 180 average time/residue: 0.0981 time to fit residues: 27.1037 Evaluate side-chains 176 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 40.0000 chunk 137 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.158926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129988 restraints weight = 14008.338| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.16 r_work: 0.3093 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12509 Z= 0.126 Angle : 0.463 9.411 17039 Z= 0.237 Chirality : 0.036 0.153 1974 Planarity : 0.004 0.045 2069 Dihedral : 7.407 102.406 1776 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.85 % Allowed : 12.10 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.43 (0.21), residues: 1579 helix: 2.80 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.79 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.009 0.001 TYR A 385 PHE 0.017 0.001 PHE C 146 TRP 0.018 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00267 (12509) covalent geometry : angle 0.46294 (17039) hydrogen bonds : bond 0.04842 ( 978) hydrogen bonds : angle 3.62847 ( 2892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.465 Fit side-chains REVERT: A 284 LYS cc_start: 0.8562 (mttm) cc_final: 0.8170 (mmtt) REVERT: B 248 LEU cc_start: 0.8243 (tp) cc_final: 0.7948 (mp) REVERT: B 355 ARG cc_start: 0.8400 (tmm-80) cc_final: 0.8067 (ttm170) REVERT: B 357 TYR cc_start: 0.8011 (m-80) cc_final: 0.7589 (m-80) REVERT: B 477 LEU cc_start: 0.8083 (tt) cc_final: 0.7477 (tt) REVERT: C 154 MET cc_start: 0.6959 (mmp) cc_final: 0.6558 (mmp) REVERT: C 502 MET cc_start: 0.7473 (mmp) cc_final: 0.6928 (mtp) outliers start: 23 outliers final: 18 residues processed: 170 average time/residue: 0.1004 time to fit residues: 26.1043 Evaluate side-chains 170 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130226 restraints weight = 14626.426| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.77 r_work: 0.3308 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12509 Z= 0.121 Angle : 0.457 9.550 17039 Z= 0.234 Chirality : 0.036 0.149 1974 Planarity : 0.004 0.045 2069 Dihedral : 7.322 101.854 1776 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.85 % Allowed : 12.18 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.45 (0.21), residues: 1579 helix: 2.83 (0.14), residues: 1319 sheet: None (None), residues: 0 loop : -0.82 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.009 0.001 TYR A 385 PHE 0.019 0.001 PHE B 546 TRP 0.017 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00254 (12509) covalent geometry : angle 0.45705 (17039) hydrogen bonds : bond 0.04723 ( 978) hydrogen bonds : angle 3.59179 ( 2892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.475 Fit side-chains REVERT: A 284 LYS cc_start: 0.8600 (mttm) cc_final: 0.8047 (mmtt) REVERT: B 248 LEU cc_start: 0.8291 (tp) cc_final: 0.7904 (mp) REVERT: B 355 ARG cc_start: 0.8547 (tmm-80) cc_final: 0.8156 (ttm170) REVERT: B 357 TYR cc_start: 0.8166 (m-80) cc_final: 0.7670 (m-80) REVERT: B 485 GLN cc_start: 0.8015 (mp10) cc_final: 0.7529 (mp10) REVERT: C 154 MET cc_start: 0.6918 (mmp) cc_final: 0.6543 (mmp) REVERT: C 502 MET cc_start: 0.7607 (mmp) cc_final: 0.6940 (mtp) outliers start: 23 outliers final: 21 residues processed: 173 average time/residue: 0.1006 time to fit residues: 26.6803 Evaluate side-chains 175 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 70 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.163346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128212 restraints weight = 14583.243| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.60 r_work: 0.3321 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12509 Z= 0.123 Angle : 0.464 9.604 17039 Z= 0.237 Chirality : 0.036 0.150 1974 Planarity : 0.004 0.045 2069 Dihedral : 7.294 101.904 1776 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.69 % Allowed : 12.58 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.48 (0.21), residues: 1579 helix: 2.87 (0.14), residues: 1313 sheet: None (None), residues: 0 loop : -0.87 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.008 0.001 TYR A 385 PHE 0.024 0.001 PHE C 146 TRP 0.020 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00260 (12509) covalent geometry : angle 0.46406 (17039) hydrogen bonds : bond 0.04758 ( 978) hydrogen bonds : angle 3.59224 ( 2892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.489 Fit side-chains REVERT: A 284 LYS cc_start: 0.8546 (mttm) cc_final: 0.7961 (mmtt) REVERT: A 480 MET cc_start: 0.6707 (ttm) cc_final: 0.6322 (ttm) REVERT: B 248 LEU cc_start: 0.8246 (tp) cc_final: 0.7829 (mp) REVERT: B 355 ARG cc_start: 0.8541 (tmm-80) cc_final: 0.8132 (ttm170) REVERT: B 357 TYR cc_start: 0.8109 (m-80) cc_final: 0.7587 (m-80) REVERT: B 485 GLN cc_start: 0.8013 (mp10) cc_final: 0.7489 (mp10) REVERT: C 154 MET cc_start: 0.6849 (mmp) cc_final: 0.6501 (mmp) REVERT: C 502 MET cc_start: 0.7540 (mmp) cc_final: 0.6824 (mtp) outliers start: 21 outliers final: 21 residues processed: 171 average time/residue: 0.1050 time to fit residues: 27.1110 Evaluate side-chains 175 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 128 optimal weight: 0.9990 chunk 1 optimal weight: 40.0000 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.163882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128746 restraints weight = 14634.235| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.60 r_work: 0.3340 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12509 Z= 0.121 Angle : 0.466 10.984 17039 Z= 0.237 Chirality : 0.036 0.148 1974 Planarity : 0.004 0.045 2069 Dihedral : 7.238 101.484 1776 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.77 % Allowed : 12.58 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.51 (0.21), residues: 1579 helix: 2.90 (0.14), residues: 1312 sheet: None (None), residues: 0 loop : -0.87 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.009 0.001 TYR A 385 PHE 0.023 0.001 PHE C 146 TRP 0.020 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00253 (12509) covalent geometry : angle 0.46569 (17039) hydrogen bonds : bond 0.04650 ( 978) hydrogen bonds : angle 3.56498 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.60 seconds wall clock time: 54 minutes 7.31 seconds (3247.31 seconds total)