Starting phenix.real_space_refine on Wed May 14 19:21:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzd_41755/05_2025/8tzd_41755_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzd_41755/05_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_41755/05_2025/8tzd_41755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzd_41755/05_2025/8tzd_41755.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzd_41755/05_2025/8tzd_41755_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzd_41755/05_2025/8tzd_41755_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 7} 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: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} 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: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} 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: 4.67, per 1000 atoms: 0.38 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: 3.17 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.03 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: 3.79 Time building geometry restraints manager: 3.70 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 622 or resid 701)) selection = (chain 'B' and (resid 90 through 421 or resid 434 through 622 or resid 701)) selection = (chain 'C' and (resid 90 through 421 or resid 434 through 622 or resid 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: 6.930 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 5.230 Set scattering table: 0.000 Process input model: 24.720 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.240 ------------------------------------------------------------------------------- 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 : 3.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP C 316 HIS 0.003 0.001 HIS A 132 PHE 0.017 0.001 PHE B 413 TYR 0.008 0.001 TYR B 231 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.13349 ( 978) hydrogen bonds : angle 5.10205 ( 2892) covalent geometry : bond 0.00950 (12509) covalent geometry : angle 0.58014 (17039) *********************** 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 : 1.257 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: 0.2074 time to fit residues: 68.9399 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 : 1.200 ------------------------------------------------------------------------------- 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 133 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.160468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130378 restraints weight = 13922.015| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.11 r_work: 0.3072 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12509 Z= 0.145 Angle : 0.499 6.988 17039 Z= 0.262 Chirality : 0.038 0.150 1974 Planarity : 0.004 0.051 2069 Dihedral : 10.329 163.889 1780 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.37 % Allowed : 7.26 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.21), residues: 1579 helix: 2.61 (0.14), residues: 1315 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.003 0.001 HIS C 394 PHE 0.015 0.001 PHE B 413 TYR 0.012 0.001 TYR A 385 ARG 0.003 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 978) hydrogen bonds : angle 3.94484 ( 2892) covalent geometry : bond 0.00308 (12509) covalent geometry : angle 0.49903 (17039) *********************** 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 199 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.230 Fit side-chains REVERT: A 284 LYS cc_start: 0.8575 (mttm) cc_final: 0.8175 (mmtt) REVERT: B 154 MET cc_start: 0.7414 (tpt) cc_final: 0.6851 (tpt) REVERT: B 305 MET cc_start: 0.7900 (mmt) cc_final: 0.7680 (mmp) REVERT: B 355 ARG cc_start: 0.8486 (tmm-80) cc_final: 0.8082 (ttm170) REVERT: B 357 TYR cc_start: 0.7983 (m-80) cc_final: 0.7743 (m-80) REVERT: B 482 ASP cc_start: 0.8983 (t0) cc_final: 0.8742 (t0) REVERT: C 154 MET cc_start: 0.6675 (mmp) cc_final: 0.6305 (mmp) REVERT: C 502 MET cc_start: 0.7605 (mmp) cc_final: 0.7127 (mtp) REVERT: C 562 SER cc_start: 0.8763 (t) cc_final: 0.8526 (m) outliers start: 17 outliers final: 12 residues processed: 194 average time/residue: 0.2032 time to fit residues: 59.9236 Evaluate side-chains 179 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 230 VAL Chi-restraints excluded: chain B residue 245 LEU 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 130 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 23 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: C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.161118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131865 restraints weight = 14135.310| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.35 r_work: 0.3094 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12509 Z= 0.130 Angle : 0.460 8.069 17039 Z= 0.240 Chirality : 0.037 0.146 1974 Planarity : 0.004 0.045 2069 Dihedral : 8.629 127.569 1779 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.37 % Allowed : 9.76 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.21), residues: 1579 helix: 2.71 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.59 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 316 HIS 0.003 0.001 HIS B 288 PHE 0.017 0.001 PHE B 546 TYR 0.013 0.001 TYR A 564 ARG 0.003 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 978) hydrogen bonds : angle 3.76953 ( 2892) covalent geometry : bond 0.00272 (12509) covalent geometry : angle 0.46047 (17039) *********************** 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 187 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.232 Fit side-chains REVERT: A 284 LYS cc_start: 0.8611 (mttm) cc_final: 0.8213 (mmtt) REVERT: B 248 LEU cc_start: 0.8357 (tp) cc_final: 0.7927 (mp) REVERT: B 305 MET cc_start: 0.7817 (mmt) cc_final: 0.7358 (mmp) REVERT: B 355 ARG cc_start: 0.8453 (tmm-80) cc_final: 0.7911 (ttm170) REVERT: B 357 TYR cc_start: 0.7981 (m-80) cc_final: 0.7684 (m-80) REVERT: B 360 TYR cc_start: 0.8119 (m-10) cc_final: 0.7899 (m-80) REVERT: B 482 ASP cc_start: 0.8945 (t0) cc_final: 0.8599 (t0) REVERT: C 154 MET cc_start: 0.6838 (mmp) cc_final: 0.6446 (mmp) REVERT: C 502 MET cc_start: 0.7639 (mmp) cc_final: 0.7174 (mtp) REVERT: C 562 SER cc_start: 0.8757 (t) cc_final: 0.8530 (m) outliers start: 17 outliers final: 11 residues processed: 182 average time/residue: 0.1995 time to fit residues: 55.0365 Evaluate side-chains 172 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR 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 98 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS C 423 ASN C 551 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.159325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3460 r_free = 0.3460 target = 0.130298 restraints weight = 13978.111| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.36 r_work: 0.3103 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2007 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 : 0.455 8.380 17039 Z= 0.236 Chirality : 0.036 0.143 1974 Planarity : 0.004 0.044 2069 Dihedral : 7.952 107.558 1776 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.45 % Allowed : 10.32 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.21), residues: 1579 helix: 2.76 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.68 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 178 HIS 0.003 0.001 HIS B 288 PHE 0.016 0.001 PHE C 146 TYR 0.007 0.001 TYR A 385 ARG 0.001 0.000 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 978) hydrogen bonds : angle 3.69583 ( 2892) covalent geometry : bond 0.00264 (12509) covalent geometry : angle 0.45501 (17039) *********************** 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 183 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.351 Fit side-chains REVERT: A 284 LYS cc_start: 0.8579 (mttm) cc_final: 0.8114 (mmtt) REVERT: B 248 LEU cc_start: 0.8400 (tp) cc_final: 0.7906 (mp) REVERT: B 305 MET cc_start: 0.7887 (mmt) cc_final: 0.7357 (mmp) REVERT: B 355 ARG cc_start: 0.8433 (tmm-80) cc_final: 0.7982 (ttm170) REVERT: B 357 TYR cc_start: 0.7965 (m-80) cc_final: 0.7625 (m-80) REVERT: C 154 MET cc_start: 0.6802 (mmp) cc_final: 0.6320 (mmp) REVERT: C 502 MET cc_start: 0.7573 (mmp) cc_final: 0.7037 (mtp) REVERT: C 562 SER cc_start: 0.8803 (t) cc_final: 0.8574 (m) outliers start: 18 outliers final: 14 residues processed: 177 average time/residue: 0.2233 time to fit residues: 59.5679 Evaluate side-chains 175 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR 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 6 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 131 optimal weight: 0.0030 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN C 423 ASN C 551 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.159960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131322 restraints weight = 13950.571| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.11 r_work: 0.3121 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12509 Z= 0.121 Angle : 0.450 8.800 17039 Z= 0.232 Chirality : 0.036 0.142 1974 Planarity : 0.004 0.044 2069 Dihedral : 7.646 101.079 1776 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.69 % Allowed : 10.89 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.21), residues: 1579 helix: 2.82 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.71 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 178 HIS 0.002 0.000 HIS B 288 PHE 0.018 0.001 PHE B 546 TYR 0.009 0.001 TYR A 564 ARG 0.002 0.000 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 978) hydrogen bonds : angle 3.61721 ( 2892) covalent geometry : bond 0.00251 (12509) covalent geometry : angle 0.44993 (17039) *********************** 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 187 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.226 Fit side-chains REVERT: A 284 LYS cc_start: 0.8585 (mttm) cc_final: 0.8161 (mmtt) REVERT: B 248 LEU cc_start: 0.8238 (tp) cc_final: 0.7922 (mp) REVERT: B 305 MET cc_start: 0.7855 (mmt) cc_final: 0.7342 (mmp) REVERT: B 355 ARG cc_start: 0.8432 (tmm-80) cc_final: 0.7994 (ttm170) REVERT: B 357 TYR cc_start: 0.7925 (m-80) cc_final: 0.7581 (m-80) REVERT: B 482 ASP cc_start: 0.8820 (t0) cc_final: 0.8508 (t0) REVERT: C 154 MET cc_start: 0.6905 (mmp) cc_final: 0.6474 (mmp) REVERT: C 502 MET cc_start: 0.7449 (mmp) cc_final: 0.6920 (mtp) REVERT: C 562 SER cc_start: 0.8758 (t) cc_final: 0.8550 (m) outliers start: 21 outliers final: 14 residues processed: 181 average time/residue: 0.1999 time to fit residues: 54.8077 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 : 1.314 ------------------------------------------------------------------------------- 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 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 189 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 58 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 80 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.162087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133145 restraints weight = 14180.202| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.26 r_work: 0.3100 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12509 Z= 0.120 Angle : 0.447 9.077 17039 Z= 0.231 Chirality : 0.036 0.142 1974 Planarity : 0.004 0.044 2069 Dihedral : 7.523 100.882 1776 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.69 % Allowed : 11.05 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.21), residues: 1579 helix: 2.83 (0.14), residues: 1321 sheet: None (None), residues: 0 loop : -0.71 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 178 HIS 0.003 0.000 HIS B 288 PHE 0.028 0.001 PHE A 146 TYR 0.006 0.001 TYR A 385 ARG 0.005 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 978) hydrogen bonds : angle 3.60804 ( 2892) covalent geometry : bond 0.00248 (12509) covalent geometry : angle 0.44663 (17039) *********************** 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 186 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.260 Fit side-chains REVERT: A 154 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6778 (tpp) REVERT: A 284 LYS cc_start: 0.8613 (mttm) cc_final: 0.8197 (mmtt) REVERT: B 248 LEU cc_start: 0.8231 (tp) cc_final: 0.7948 (mp) REVERT: B 305 MET cc_start: 0.7899 (mmt) cc_final: 0.7397 (mmp) REVERT: B 355 ARG cc_start: 0.8450 (tmm-80) cc_final: 0.8008 (ttm170) REVERT: B 357 TYR cc_start: 0.7974 (m-80) cc_final: 0.7589 (m-80) REVERT: C 154 MET cc_start: 0.6972 (mmp) cc_final: 0.6524 (mmp) REVERT: C 329 MET cc_start: 0.8598 (mtt) cc_final: 0.7999 (mtt) REVERT: C 502 MET cc_start: 0.7490 (mmp) cc_final: 0.6957 (mtp) outliers start: 21 outliers final: 15 residues processed: 177 average time/residue: 0.2159 time to fit residues: 57.9088 Evaluate side-chains 174 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 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 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 189 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain C residue 413 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 45 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 127 optimal weight: 0.6980 chunk 106 optimal weight: 30.0000 chunk 152 optimal weight: 0.9990 chunk 19 optimal weight: 0.0010 chunk 140 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN C 423 ASN C 551 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.162173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133403 restraints weight = 13991.252| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.22 r_work: 0.3143 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12509 Z= 0.110 Angle : 0.443 8.508 17039 Z= 0.225 Chirality : 0.035 0.137 1974 Planarity : 0.003 0.043 2069 Dihedral : 7.334 99.342 1776 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.37 % Allowed : 11.45 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.21), residues: 1579 helix: 2.91 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.71 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 178 HIS 0.002 0.000 HIS B 288 PHE 0.017 0.001 PHE B 546 TYR 0.005 0.001 TYR B 483 ARG 0.004 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 978) hydrogen bonds : angle 3.50786 ( 2892) covalent geometry : bond 0.00220 (12509) covalent geometry : angle 0.44304 (17039) *********************** 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 185 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.222 Fit side-chains REVERT: A 284 LYS cc_start: 0.8618 (mttm) cc_final: 0.8225 (mmtt) REVERT: B 248 LEU cc_start: 0.8237 (tp) cc_final: 0.7962 (mp) REVERT: B 305 MET cc_start: 0.7844 (mmt) cc_final: 0.7529 (mmt) REVERT: B 355 ARG cc_start: 0.8418 (tmm-80) cc_final: 0.8019 (ttm170) REVERT: B 357 TYR cc_start: 0.7940 (m-80) cc_final: 0.7563 (m-80) REVERT: B 477 LEU cc_start: 0.8027 (tt) cc_final: 0.7375 (tt) REVERT: C 154 MET cc_start: 0.7133 (mmp) cc_final: 0.6740 (mmp) REVERT: C 502 MET cc_start: 0.7452 (mmp) cc_final: 0.6946 (mtp) outliers start: 17 outliers final: 14 residues processed: 179 average time/residue: 0.2004 time to fit residues: 54.0682 Evaluate side-chains 176 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 413 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 128 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.163471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133212 restraints weight = 14134.420| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.18 r_work: 0.3366 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2559 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= 0.115 Angle : 0.448 9.573 17039 Z= 0.228 Chirality : 0.036 0.148 1974 Planarity : 0.003 0.041 2069 Dihedral : 7.298 100.550 1776 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.29 % Allowed : 12.34 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.21), residues: 1579 helix: 2.94 (0.14), residues: 1316 sheet: None (None), residues: 0 loop : -0.73 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 150 HIS 0.002 0.000 HIS B 288 PHE 0.031 0.001 PHE A 146 TYR 0.005 0.001 TYR A 385 ARG 0.003 0.000 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 978) hydrogen bonds : angle 3.52092 ( 2892) covalent geometry : bond 0.00235 (12509) covalent geometry : angle 0.44766 (17039) *********************** 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 182 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.386 Fit side-chains REVERT: A 284 LYS cc_start: 0.8550 (mttm) cc_final: 0.8216 (mmtt) REVERT: A 480 MET cc_start: 0.6886 (ttm) cc_final: 0.6498 (ttm) REVERT: B 248 LEU cc_start: 0.8231 (tp) cc_final: 0.7999 (mp) REVERT: B 305 MET cc_start: 0.7786 (mmt) cc_final: 0.7459 (mmt) REVERT: B 355 ARG cc_start: 0.8478 (tmm-80) cc_final: 0.8032 (ttm170) REVERT: B 357 TYR cc_start: 0.8090 (m-80) cc_final: 0.7678 (m-80) REVERT: B 477 LEU cc_start: 0.8192 (tt) cc_final: 0.7488 (tt) REVERT: B 482 ASP cc_start: 0.8823 (t0) cc_final: 0.8516 (t0) REVERT: B 485 GLN cc_start: 0.7868 (mp10) cc_final: 0.7472 (mp10) REVERT: C 154 MET cc_start: 0.7107 (mmp) cc_final: 0.6698 (mmp) REVERT: C 176 TRP cc_start: 0.6844 (t-100) cc_final: 0.6554 (t60) REVERT: C 502 MET cc_start: 0.7492 (mmp) cc_final: 0.6903 (mtp) outliers start: 16 outliers final: 15 residues processed: 178 average time/residue: 0.2097 time to fit residues: 56.8023 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 : 1.228 ------------------------------------------------------------------------------- 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 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 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 435 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 52 optimal weight: 0.0470 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.166507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131416 restraints weight = 14542.239| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.60 r_work: 0.3363 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2656 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= 0.111 Angle : 0.448 9.614 17039 Z= 0.227 Chirality : 0.035 0.145 1974 Planarity : 0.003 0.040 2069 Dihedral : 7.233 100.541 1776 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.45 % Allowed : 12.26 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.21), residues: 1579 helix: 2.98 (0.14), residues: 1315 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 178 HIS 0.002 0.000 HIS B 288 PHE 0.019 0.001 PHE C 146 TYR 0.008 0.001 TYR A 385 ARG 0.003 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 978) hydrogen bonds : angle 3.49514 ( 2892) covalent geometry : bond 0.00225 (12509) covalent geometry : angle 0.44808 (17039) *********************** 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 180 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.239 Fit side-chains REVERT: A 163 ARG cc_start: 0.7638 (tmm-80) cc_final: 0.6834 (ttp80) REVERT: A 284 LYS cc_start: 0.8481 (mttm) cc_final: 0.7882 (mmtt) REVERT: A 480 MET cc_start: 0.6529 (ttm) cc_final: 0.6147 (ttm) REVERT: B 248 LEU cc_start: 0.8259 (tp) cc_final: 0.7786 (mp) REVERT: B 305 MET cc_start: 0.8126 (mmt) cc_final: 0.7814 (mmt) REVERT: B 355 ARG cc_start: 0.8404 (tmm-80) cc_final: 0.7999 (ttm170) REVERT: B 357 TYR cc_start: 0.8008 (m-80) cc_final: 0.7560 (m-80) REVERT: B 482 ASP cc_start: 0.8861 (t0) cc_final: 0.8584 (t0) REVERT: B 617 MET cc_start: 0.8785 (ttp) cc_final: 0.8577 (ttm) REVERT: C 154 MET cc_start: 0.6866 (mmp) cc_final: 0.6515 (mmp) REVERT: C 502 MET cc_start: 0.7500 (mmp) cc_final: 0.6636 (mtp) outliers start: 18 outliers final: 17 residues processed: 175 average time/residue: 0.2060 time to fit residues: 54.5089 Evaluate side-chains 176 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 40.0000 chunk 128 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 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 = 0.3860 r_free = 0.3860 target = 0.163960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128693 restraints weight = 14599.322| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.61 r_work: 0.3327 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2643 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= 0.122 Angle : 0.463 9.552 17039 Z= 0.235 Chirality : 0.036 0.150 1974 Planarity : 0.003 0.039 2069 Dihedral : 7.285 102.056 1776 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.53 % Allowed : 12.18 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.21), residues: 1579 helix: 2.90 (0.14), residues: 1321 sheet: None (None), residues: 0 loop : -0.72 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 178 HIS 0.003 0.001 HIS B 288 PHE 0.024 0.001 PHE B 138 TYR 0.010 0.001 TYR A 385 ARG 0.004 0.000 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 978) hydrogen bonds : angle 3.55350 ( 2892) covalent geometry : bond 0.00259 (12509) covalent geometry : angle 0.46341 (17039) ********************** 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 178 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.251 Fit side-chains REVERT: A 163 ARG cc_start: 0.7646 (tmm-80) cc_final: 0.6828 (ttp80) REVERT: A 284 LYS cc_start: 0.8515 (mttm) cc_final: 0.7929 (mmtt) REVERT: A 480 MET cc_start: 0.6647 (ttm) cc_final: 0.6119 (ttm) REVERT: B 248 LEU cc_start: 0.8299 (tp) cc_final: 0.7837 (mp) REVERT: B 305 MET cc_start: 0.8129 (mmt) cc_final: 0.7622 (mmp) REVERT: B 355 ARG cc_start: 0.8493 (tmm-80) cc_final: 0.8020 (ttm170) REVERT: B 357 TYR cc_start: 0.8061 (m-80) cc_final: 0.7580 (m-80) REVERT: B 482 ASP cc_start: 0.8862 (t0) cc_final: 0.8607 (t0) REVERT: C 154 MET cc_start: 0.6889 (mmp) cc_final: 0.6533 (mmp) outliers start: 19 outliers final: 18 residues processed: 173 average time/residue: 0.2007 time to fit residues: 52.8351 Evaluate side-chains 173 residues out of total 1325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 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 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 130 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.160698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125450 restraints weight = 14560.759| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.59 r_work: 0.3285 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12509 Z= 0.148 Angle : 0.494 11.799 17039 Z= 0.253 Chirality : 0.037 0.158 1974 Planarity : 0.004 0.039 2069 Dihedral : 7.483 104.616 1776 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.53 % Allowed : 12.34 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.21), residues: 1579 helix: 2.77 (0.14), residues: 1318 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 178 HIS 0.003 0.001 HIS B 288 PHE 0.025 0.001 PHE B 138 TYR 0.011 0.001 TYR A 385 ARG 0.004 0.000 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 978) hydrogen bonds : angle 3.70199 ( 2892) covalent geometry : bond 0.00334 (12509) covalent geometry : angle 0.49401 (17039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6208.08 seconds wall clock time: 108 minutes 17.93 seconds (6497.93 seconds total)