Starting phenix.real_space_refine on Sun May 11 22:30:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3z_61128/05_2025/9j3z_61128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3z_61128/05_2025/9j3z_61128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j3z_61128/05_2025/9j3z_61128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3z_61128/05_2025/9j3z_61128.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3z_61128/05_2025/9j3z_61128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3z_61128/05_2025/9j3z_61128.cif" } resolution = 3.5 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= 0.000 sd= 0.013 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 4 5.49 5 S 42 5.16 5 C 5624 2.51 5 N 1332 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8491 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4150 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 554} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 384 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 4135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4135 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 21, 'TRANS': 548} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.39, per 1000 atoms: 0.63 Number of scatterers: 8491 At special positions: 0 Unit cell: (124.12, 98.44, 73.83, 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 42 16.00 P 4 15.00 O 1489 8.00 N 1332 7.00 C 5624 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 Links applied NAG-ASN " NAG A 903 " - " ASN A 309 " " NAG B 903 " - " ASN B 309 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 38 through 41 removed outlier: 3.612A pdb=" N ARG A 41 " --> pdb=" O SER A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'A' and resid 42 through 63 removed outlier: 3.904A pdb=" N VAL A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 92 removed outlier: 5.573A pdb=" N LEU A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.922A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.861A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 removed outlier: 3.704A pdb=" N TYR A 165 " --> pdb=" O TYR A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 166 through 197 removed outlier: 4.527A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.878A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.708A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.478A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.807A pdb=" N SER A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 302 removed outlier: 4.509A pdb=" N LEU A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.762A pdb=" N GLY A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 367 removed outlier: 4.314A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 373 through 404 removed outlier: 4.294A pdb=" N TYR A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 435 removed outlier: 3.951A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 473 removed outlier: 3.739A pdb=" N GLY A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.684A pdb=" N PHE A 514 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 515 " --> pdb=" O SER A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 515' Processing helix chain 'A' and resid 517 through 546 removed outlier: 3.606A pdb=" N MET A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 682 removed outlier: 3.751A pdb=" N VAL A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU A 660 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 666 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS A 676 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 680 " --> pdb=" O CYS A 676 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 702 Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.605A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 41 Processing helix chain 'B' and resid 42 through 62 removed outlier: 4.050A pdb=" N VAL B 53 " --> pdb=" O CYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 80 removed outlier: 3.991A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 removed outlier: 3.556A pdb=" N ALA B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 125 removed outlier: 3.567A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 129 through 141 Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.806A pdb=" N ILE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.702A pdb=" N LEU B 166 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 196 Proline residue: B 174 - end of helix Proline residue: B 182 - end of helix removed outlier: 3.972A pdb=" N PHE B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.859A pdb=" N LEU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.515A pdb=" N PHE B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.434A pdb=" N ASN B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.658A pdb=" N SER B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 307 through 322 removed outlier: 3.661A pdb=" N THR B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 339 through 366 removed outlier: 3.893A pdb=" N PHE B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix removed outlier: 4.013A pdb=" N TYR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 404 removed outlier: 3.733A pdb=" N ALA B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 435 removed outlier: 3.613A pdb=" N LEU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 474 removed outlier: 4.075A pdb=" N GLY B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 464 " --> pdb=" O TRP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 502 removed outlier: 3.825A pdb=" N GLY B 482 " --> pdb=" O GLN B 478 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 517 through 546 removed outlier: 3.715A pdb=" N MET B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 681 removed outlier: 3.620A pdb=" N VAL B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 665 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 671 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS B 676 " --> pdb=" O ASN B 672 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 680 " --> pdb=" O CYS B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 702 removed outlier: 3.554A pdb=" N VAL B 690 " --> pdb=" O GLY B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 712 removed outlier: 4.066A pdb=" N ILE B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1959 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: 2.39 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1427 1.33 - 1.45: 2253 1.45 - 1.57: 4917 1.57 - 1.70: 8 1.70 - 1.82: 68 Bond restraints: 8673 Sorted by residual: bond pdb=" C21 POV A 901 " pdb=" O21 POV A 901 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C31 POV A 901 " pdb=" O31 POV A 901 " ideal model delta sigma weight residual 1.327 1.450 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C PHE A 367 " pdb=" N PRO A 368 " ideal model delta sigma weight residual 1.330 1.364 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" C1 NAG B 903 " pdb=" O5 NAG B 903 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.53e+00 ... (remaining 8668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 11467 2.90 - 5.81: 279 5.81 - 8.71: 43 8.71 - 11.61: 16 11.61 - 14.52: 5 Bond angle restraints: 11810 Sorted by residual: angle pdb=" N GLY B 462 " pdb=" CA GLY B 462 " pdb=" C GLY B 462 " ideal model delta sigma weight residual 112.77 120.28 -7.51 1.28e+00 6.10e-01 3.44e+01 angle pdb=" C ALA A 62 " pdb=" N ASN A 63 " pdb=" CA ASN A 63 " ideal model delta sigma weight residual 121.54 131.15 -9.61 1.91e+00 2.74e-01 2.53e+01 angle pdb=" C ALA B 62 " pdb=" N ASN B 63 " pdb=" CA ASN B 63 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C LEU A 103 " pdb=" N TYR A 104 " pdb=" CA TYR A 104 " ideal model delta sigma weight residual 121.14 112.85 8.29 1.75e+00 3.27e-01 2.24e+01 angle pdb=" CA LYS A 303 " pdb=" CB LYS A 303 " pdb=" CG LYS A 303 " ideal model delta sigma weight residual 114.10 123.48 -9.38 2.00e+00 2.50e-01 2.20e+01 ... (remaining 11805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 4529 22.90 - 45.81: 444 45.81 - 68.71: 68 68.71 - 91.62: 17 91.62 - 114.52: 33 Dihedral angle restraints: 5091 sinusoidal: 1769 harmonic: 3322 Sorted by residual: dihedral pdb=" N2 NAG A 903 " pdb=" C1 NAG A 903 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sinusoidal sigma weight residual -178.19 -63.67 -114.52 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" N2 NAG B 903 " pdb=" C1 NAG B 903 " pdb=" C2 NAG B 903 " pdb=" O5 NAG B 903 " ideal model delta sinusoidal sigma weight residual -178.19 -64.17 -114.02 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" C3 NAG A 903 " pdb=" C1 NAG A 903 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sinusoidal sigma weight residual -55.55 58.16 -113.71 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 5088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1374 0.139 - 0.279: 32 0.279 - 0.418: 3 0.418 - 0.557: 0 0.557 - 0.697: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CG LEU A 279 " pdb=" CB LEU A 279 " pdb=" CD1 LEU A 279 " pdb=" CD2 LEU A 279 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 309 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE A 116 " pdb=" CA ILE A 116 " pdb=" CG1 ILE A 116 " pdb=" CG2 ILE A 116 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1407 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 348 " 0.023 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C VAL A 348 " -0.080 2.00e-02 2.50e+03 pdb=" O VAL A 348 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE A 349 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 77 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C VAL A 77 " -0.062 2.00e-02 2.50e+03 pdb=" O VAL A 77 " 0.023 2.00e-02 2.50e+03 pdb=" N SER A 78 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 326 " -0.052 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 327 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " -0.044 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 572 2.73 - 3.27: 8844 3.27 - 3.81: 13940 3.81 - 4.36: 15927 4.36 - 4.90: 27262 Nonbonded interactions: 66545 Sorted by model distance: nonbonded pdb=" O PRO A 138 " pdb=" OG1 THR A 142 " model vdw 2.187 3.040 nonbonded pdb=" O SER A 251 " pdb=" OG SER A 255 " model vdw 2.248 3.040 nonbonded pdb=" O ILE B 331 " pdb=" OG1 THR B 334 " model vdw 2.265 3.040 nonbonded pdb=" O LEU A 300 " pdb=" NZ LYS A 303 " model vdw 2.268 3.120 nonbonded pdb=" O VAL B 117 " pdb=" OG1 THR B 121 " model vdw 2.272 3.040 ... (remaining 66540 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 36 through 194 or (resid 195 through 196 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 368 or (resid 369 t \ hrough 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ through 714 or (resid 715 through 717 and (name N or name CA or name C or name \ O or name CB )) or resid 901 through 903)) selection = (chain 'B' and (resid 36 through 406 or (resid 407 through 421 and (name N or na \ me CA or name C or name O or name CB )) or resid 422 through 447 or (resid 448 t \ hrough 450 and (name N or name CA or name C or name O or name CB )) or resid 451 \ through 666 or (resid 667 and (name N or name CA or name C or name O or name CB \ )) or resid 668 through 717 or resid 901 through 903)) } 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 group one per residue 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: 0.690 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.070 Find NCS groups from input model: 0.410 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 8675 Z= 0.262 Angle : 1.141 14.516 11816 Z= 0.629 Chirality : 0.061 0.697 1410 Planarity : 0.007 0.081 1458 Dihedral : 21.166 114.522 2947 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.08 % Favored : 96.65 % Rotamer: Outliers : 0.77 % Allowed : 32.26 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1136 helix: -0.55 (0.15), residues: 885 sheet: None (None), residues: 0 loop : -1.66 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 679 HIS 0.011 0.003 HIS B 310 PHE 0.046 0.003 PHE B 699 TYR 0.019 0.002 TYR B 170 ARG 0.009 0.001 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.01257 ( 2) link_NAG-ASN : angle 4.04099 ( 6) hydrogen bonds : bond 0.20759 ( 655) hydrogen bonds : angle 6.17561 ( 1959) covalent geometry : bond 0.00547 ( 8673) covalent geometry : angle 1.13784 (11810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 189 time to evaluate : 0.980 Fit side-chains REVERT: A 280 ILE cc_start: 0.8503 (mm) cc_final: 0.8043 (mp) REVERT: A 358 MET cc_start: 0.8958 (mmm) cc_final: 0.8751 (tpp) REVERT: B 47 LEU cc_start: 0.8252 (mm) cc_final: 0.7915 (mt) outliers start: 6 outliers final: 3 residues processed: 191 average time/residue: 0.1669 time to fit residues: 46.0987 Evaluate side-chains 179 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 711 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0870 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 40.0000 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 216 GLN A 310 HIS B 181 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.183590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143697 restraints weight = 12462.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147763 restraints weight = 7076.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150242 restraints weight = 5032.175| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8675 Z= 0.153 Angle : 0.687 11.482 11816 Z= 0.348 Chirality : 0.045 0.253 1410 Planarity : 0.005 0.061 1458 Dihedral : 13.075 107.736 1385 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.46 % Favored : 97.27 % Rotamer: Outliers : 3.47 % Allowed : 26.86 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1136 helix: 0.97 (0.17), residues: 913 sheet: None (None), residues: 0 loop : -1.62 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 460 HIS 0.005 0.001 HIS B 310 PHE 0.026 0.002 PHE B 221 TYR 0.022 0.001 TYR B 455 ARG 0.003 0.001 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.01062 ( 2) link_NAG-ASN : angle 3.92567 ( 6) hydrogen bonds : bond 0.04874 ( 655) hydrogen bonds : angle 4.23600 ( 1959) covalent geometry : bond 0.00326 ( 8673) covalent geometry : angle 0.68119 (11810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 270 ARG cc_start: 0.2397 (mpt-90) cc_final: 0.1891 (mtt180) REVERT: A 299 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 381 ASN cc_start: 0.7224 (t0) cc_final: 0.6850 (t0) REVERT: B 130 ARG cc_start: 0.6831 (mtp180) cc_final: 0.6229 (ttm110) REVERT: B 216 GLN cc_start: 0.7765 (mt0) cc_final: 0.7559 (mt0) REVERT: B 296 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7093 (mm-30) REVERT: B 455 TYR cc_start: 0.7687 (m-80) cc_final: 0.7472 (m-80) outliers start: 27 outliers final: 11 residues processed: 207 average time/residue: 0.1822 time to fit residues: 53.3177 Evaluate side-chains 186 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 711 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 110 optimal weight: 30.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.181321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141107 restraints weight = 12627.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145124 restraints weight = 7118.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.147677 restraints weight = 5089.088| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8675 Z= 0.143 Angle : 0.647 9.382 11816 Z= 0.325 Chirality : 0.043 0.192 1410 Planarity : 0.005 0.059 1458 Dihedral : 11.798 93.701 1382 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.46 % Favored : 97.27 % Rotamer: Outliers : 4.63 % Allowed : 25.19 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1136 helix: 1.65 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -1.39 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 460 HIS 0.008 0.002 HIS B 310 PHE 0.021 0.001 PHE B 221 TYR 0.019 0.001 TYR B 455 ARG 0.002 0.000 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00761 ( 2) link_NAG-ASN : angle 4.67751 ( 6) hydrogen bonds : bond 0.04505 ( 655) hydrogen bonds : angle 4.02174 ( 1959) covalent geometry : bond 0.00316 ( 8673) covalent geometry : angle 0.63827 (11810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: A 377 TYR cc_start: 0.7074 (m-80) cc_final: 0.6814 (m-80) REVERT: A 381 ASN cc_start: 0.7271 (t0) cc_final: 0.6907 (t0) REVERT: B 130 ARG cc_start: 0.6861 (mtp180) cc_final: 0.6170 (ttm110) REVERT: B 235 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7843 (ttp80) REVERT: B 296 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7211 (mm-30) REVERT: B 358 MET cc_start: 0.8064 (mmm) cc_final: 0.7802 (ttm) REVERT: B 390 SER cc_start: 0.8988 (t) cc_final: 0.8172 (p) REVERT: B 420 ILE cc_start: 0.8496 (tt) cc_final: 0.8263 (tp) REVERT: B 695 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.7008 (t80) outliers start: 36 outliers final: 25 residues processed: 207 average time/residue: 0.1786 time to fit residues: 52.1427 Evaluate side-chains 198 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 695 PHE Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 695 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 100 optimal weight: 30.0000 chunk 18 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 310 HIS ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139953 restraints weight = 12646.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143984 restraints weight = 7205.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.146540 restraints weight = 5179.395| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8675 Z= 0.147 Angle : 0.654 9.758 11816 Z= 0.326 Chirality : 0.044 0.203 1410 Planarity : 0.005 0.065 1458 Dihedral : 11.450 91.607 1380 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.55 % Favored : 97.18 % Rotamer: Outliers : 5.01 % Allowed : 25.71 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1136 helix: 1.92 (0.17), residues: 909 sheet: None (None), residues: 0 loop : -1.39 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 432 HIS 0.007 0.001 HIS B 310 PHE 0.022 0.001 PHE B 221 TYR 0.020 0.001 TYR A 689 ARG 0.002 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 2) link_NAG-ASN : angle 4.33636 ( 6) hydrogen bonds : bond 0.04227 ( 655) hydrogen bonds : angle 4.02854 ( 1959) covalent geometry : bond 0.00333 ( 8673) covalent geometry : angle 0.64695 (11810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.890 Fit side-chains REVERT: A 299 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: A 377 TYR cc_start: 0.7057 (m-80) cc_final: 0.6812 (m-80) REVERT: A 381 ASN cc_start: 0.7180 (t0) cc_final: 0.6887 (t0) REVERT: A 384 PHE cc_start: 0.8611 (t80) cc_final: 0.8410 (t80) REVERT: B 130 ARG cc_start: 0.6858 (mtp180) cc_final: 0.6142 (ttm110) REVERT: B 390 SER cc_start: 0.9007 (t) cc_final: 0.8178 (p) REVERT: B 413 MET cc_start: 0.7145 (tpp) cc_final: 0.6834 (tpp) REVERT: B 420 ILE cc_start: 0.8530 (tt) cc_final: 0.8288 (tp) REVERT: B 430 MET cc_start: 0.7860 (mmt) cc_final: 0.7534 (mmm) REVERT: B 455 TYR cc_start: 0.7710 (m-80) cc_final: 0.7387 (m-80) outliers start: 39 outliers final: 26 residues processed: 200 average time/residue: 0.1813 time to fit residues: 51.0231 Evaluate side-chains 194 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 695 PHE Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 460 TRP Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 695 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 2 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.180770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139879 restraints weight = 12016.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144234 restraints weight = 6607.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147071 restraints weight = 4576.990| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8675 Z= 0.130 Angle : 0.661 11.686 11816 Z= 0.322 Chirality : 0.044 0.281 1410 Planarity : 0.004 0.071 1458 Dihedral : 11.136 89.824 1380 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.90 % Favored : 96.83 % Rotamer: Outliers : 5.01 % Allowed : 25.84 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.17 (0.26), residues: 1136 helix: 2.09 (0.17), residues: 909 sheet: None (None), residues: 0 loop : -1.33 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 460 HIS 0.003 0.001 HIS B 310 PHE 0.022 0.001 PHE B 221 TYR 0.018 0.001 TYR A 689 ARG 0.003 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 2) link_NAG-ASN : angle 4.24258 ( 6) hydrogen bonds : bond 0.04012 ( 655) hydrogen bonds : angle 3.93233 ( 1959) covalent geometry : bond 0.00283 ( 8673) covalent geometry : angle 0.65393 (11810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8473 (tttt) cc_final: 0.7768 (tptt) REVERT: A 286 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.5183 (tttm) REVERT: A 299 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: A 377 TYR cc_start: 0.7129 (m-80) cc_final: 0.6884 (m-80) REVERT: A 381 ASN cc_start: 0.7011 (t0) cc_final: 0.6707 (t0) REVERT: B 130 ARG cc_start: 0.6760 (mtp180) cc_final: 0.6008 (ttm110) REVERT: B 293 LEU cc_start: 0.7802 (mt) cc_final: 0.7493 (tp) REVERT: B 390 SER cc_start: 0.8987 (t) cc_final: 0.8139 (p) REVERT: B 413 MET cc_start: 0.7020 (tpp) cc_final: 0.6661 (ttt) REVERT: B 420 ILE cc_start: 0.8517 (tt) cc_final: 0.8250 (tp) REVERT: B 430 MET cc_start: 0.7853 (mmt) cc_final: 0.7554 (mmm) REVERT: B 455 TYR cc_start: 0.7745 (m-80) cc_final: 0.7465 (m-80) outliers start: 39 outliers final: 23 residues processed: 208 average time/residue: 0.1762 time to fit residues: 52.5449 Evaluate side-chains 194 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 695 PHE Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 695 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 85 optimal weight: 0.0970 chunk 105 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS B 417 ASN B 703 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139509 restraints weight = 11945.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143930 restraints weight = 6531.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146745 restraints weight = 4510.157| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8675 Z= 0.134 Angle : 0.666 10.684 11816 Z= 0.324 Chirality : 0.044 0.217 1410 Planarity : 0.004 0.071 1458 Dihedral : 10.888 89.516 1380 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.73 % Favored : 97.01 % Rotamer: Outliers : 5.01 % Allowed : 27.12 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.16 (0.26), residues: 1136 helix: 2.07 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -1.28 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 460 HIS 0.008 0.002 HIS A 716 PHE 0.022 0.001 PHE B 221 TYR 0.016 0.001 TYR A 689 ARG 0.004 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 2) link_NAG-ASN : angle 4.05445 ( 6) hydrogen bonds : bond 0.03988 ( 655) hydrogen bonds : angle 3.91910 ( 1959) covalent geometry : bond 0.00298 ( 8673) covalent geometry : angle 0.65952 (11810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8478 (tttt) cc_final: 0.7736 (tptt) REVERT: A 235 ARG cc_start: 0.7407 (mtp85) cc_final: 0.7158 (mtp85) REVERT: A 270 ARG cc_start: 0.2505 (mpt-90) cc_final: 0.2089 (mtt180) REVERT: A 299 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: A 377 TYR cc_start: 0.7046 (m-80) cc_final: 0.6770 (m-80) REVERT: A 381 ASN cc_start: 0.7044 (t0) cc_final: 0.6730 (t0) REVERT: A 432 TRP cc_start: 0.7648 (t-100) cc_final: 0.7329 (t-100) REVERT: A 691 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 130 ARG cc_start: 0.6751 (mtp180) cc_final: 0.6001 (ttm110) REVERT: B 235 ARG cc_start: 0.8031 (mtm110) cc_final: 0.7810 (ttp80) REVERT: B 296 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7308 (mm-30) REVERT: B 365 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8210 (mm) REVERT: B 390 SER cc_start: 0.9019 (t) cc_final: 0.8190 (p) REVERT: B 413 MET cc_start: 0.6866 (tpp) cc_final: 0.6618 (ttt) REVERT: B 420 ILE cc_start: 0.8515 (tt) cc_final: 0.8228 (tp) REVERT: B 430 MET cc_start: 0.7780 (mmt) cc_final: 0.7525 (mmm) REVERT: B 455 TYR cc_start: 0.7784 (m-80) cc_final: 0.7426 (m-80) outliers start: 39 outliers final: 26 residues processed: 205 average time/residue: 0.1843 time to fit residues: 53.1285 Evaluate side-chains 193 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 695 PHE Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 695 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.180133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138380 restraints weight = 12068.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142694 restraints weight = 6734.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145473 restraints weight = 4710.895| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8675 Z= 0.142 Angle : 0.683 10.068 11816 Z= 0.332 Chirality : 0.044 0.199 1410 Planarity : 0.004 0.071 1458 Dihedral : 10.758 89.656 1380 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.82 % Favored : 96.92 % Rotamer: Outliers : 5.14 % Allowed : 28.53 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.14 (0.26), residues: 1136 helix: 2.05 (0.17), residues: 915 sheet: None (None), residues: 0 loop : -1.36 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 460 HIS 0.006 0.002 HIS A 716 PHE 0.022 0.001 PHE B 221 TYR 0.014 0.001 TYR A 689 ARG 0.007 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 2) link_NAG-ASN : angle 4.06656 ( 6) hydrogen bonds : bond 0.04056 ( 655) hydrogen bonds : angle 3.95202 ( 1959) covalent geometry : bond 0.00326 ( 8673) covalent geometry : angle 0.67698 (11810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.851 Fit side-chains REVERT: A 299 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: A 377 TYR cc_start: 0.7235 (m-80) cc_final: 0.6955 (m-80) REVERT: A 381 ASN cc_start: 0.7039 (t0) cc_final: 0.6769 (t0) REVERT: A 432 TRP cc_start: 0.7715 (t-100) cc_final: 0.7440 (t-100) REVERT: A 691 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7199 (tm-30) REVERT: B 130 ARG cc_start: 0.6826 (mtp180) cc_final: 0.6058 (ttm110) REVERT: B 365 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8233 (mm) REVERT: B 390 SER cc_start: 0.8992 (t) cc_final: 0.8150 (p) REVERT: B 413 MET cc_start: 0.6810 (tpp) cc_final: 0.6567 (ttt) REVERT: B 420 ILE cc_start: 0.8473 (tt) cc_final: 0.8166 (tp) REVERT: B 455 TYR cc_start: 0.7781 (m-80) cc_final: 0.7432 (m-80) outliers start: 40 outliers final: 27 residues processed: 200 average time/residue: 0.1846 time to fit residues: 52.3955 Evaluate side-chains 193 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 695 PHE Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 695 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 103 optimal weight: 50.0000 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 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 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.177838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135864 restraints weight = 12215.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140194 restraints weight = 6800.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142891 restraints weight = 4757.809| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8675 Z= 0.163 Angle : 0.737 13.628 11816 Z= 0.357 Chirality : 0.046 0.338 1410 Planarity : 0.005 0.072 1458 Dihedral : 10.699 90.431 1380 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.99 % Favored : 96.74 % Rotamer: Outliers : 4.24 % Allowed : 30.85 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.06 (0.26), residues: 1136 helix: 1.99 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 460 HIS 0.003 0.001 HIS B 310 PHE 0.023 0.002 PHE B 332 TYR 0.013 0.001 TYR A 689 ARG 0.005 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 2) link_NAG-ASN : angle 4.16447 ( 6) hydrogen bonds : bond 0.04282 ( 655) hydrogen bonds : angle 4.05055 ( 1959) covalent geometry : bond 0.00384 ( 8673) covalent geometry : angle 0.73136 (11810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.919 Fit side-chains REVERT: A 48 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8351 (tt0) REVERT: A 270 ARG cc_start: 0.2533 (mpt-90) cc_final: 0.2028 (mtt180) REVERT: A 299 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: A 377 TYR cc_start: 0.7338 (m-80) cc_final: 0.7070 (m-80) REVERT: A 381 ASN cc_start: 0.7245 (t0) cc_final: 0.7040 (t0) REVERT: A 432 TRP cc_start: 0.7877 (t-100) cc_final: 0.7618 (t-100) REVERT: A 691 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 701 PHE cc_start: 0.6925 (m-80) cc_final: 0.6444 (m-80) REVERT: B 130 ARG cc_start: 0.6904 (mtp180) cc_final: 0.6001 (ttm110) REVERT: B 216 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7503 (mp10) REVERT: B 365 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8247 (mm) REVERT: B 390 SER cc_start: 0.8947 (t) cc_final: 0.8096 (p) REVERT: B 394 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7589 (tp) REVERT: B 413 MET cc_start: 0.6667 (tpp) cc_final: 0.6384 (ttt) REVERT: B 420 ILE cc_start: 0.8441 (tt) cc_final: 0.8132 (tp) REVERT: B 455 TYR cc_start: 0.7798 (m-80) cc_final: 0.7410 (m-80) outliers start: 33 outliers final: 27 residues processed: 187 average time/residue: 0.1710 time to fit residues: 46.1797 Evaluate side-chains 194 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 695 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 57 optimal weight: 0.0040 chunk 96 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 40.0000 chunk 97 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127844 restraints weight = 12507.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131887 restraints weight = 7039.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134517 restraints weight = 5001.167| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 8675 Z= 0.297 Angle : 0.872 14.016 11816 Z= 0.425 Chirality : 0.051 0.339 1410 Planarity : 0.005 0.071 1458 Dihedral : 11.349 101.118 1380 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.48 % Rotamer: Outliers : 4.11 % Allowed : 30.21 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1136 helix: 1.71 (0.17), residues: 907 sheet: None (None), residues: 0 loop : -1.46 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 460 HIS 0.004 0.001 HIS B 310 PHE 0.039 0.003 PHE B 185 TYR 0.021 0.002 TYR A 165 ARG 0.002 0.001 ARG A 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 2) link_NAG-ASN : angle 4.35816 ( 6) hydrogen bonds : bond 0.05332 ( 655) hydrogen bonds : angle 4.50122 ( 1959) covalent geometry : bond 0.00722 ( 8673) covalent geometry : angle 0.86678 (11810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.906 Fit side-chains REVERT: A 48 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8421 (tt0) REVERT: A 194 LYS cc_start: 0.8517 (tttt) cc_final: 0.7677 (tptt) REVERT: A 222 MET cc_start: 0.8513 (tpp) cc_final: 0.8312 (tpp) REVERT: A 299 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: A 377 TYR cc_start: 0.7838 (m-80) cc_final: 0.7590 (m-80) REVERT: A 691 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7232 (tm-30) REVERT: B 365 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8387 (mm) REVERT: B 413 MET cc_start: 0.6631 (tpp) cc_final: 0.6370 (ttt) REVERT: B 420 ILE cc_start: 0.8577 (tt) cc_final: 0.8312 (tp) REVERT: B 430 MET cc_start: 0.7910 (mmt) cc_final: 0.7558 (mmm) REVERT: B 455 TYR cc_start: 0.7953 (m-80) cc_final: 0.7632 (m-80) outliers start: 32 outliers final: 24 residues processed: 183 average time/residue: 0.1664 time to fit residues: 44.0382 Evaluate side-chains 179 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 670 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 67 optimal weight: 0.0670 chunk 97 optimal weight: 6.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 181 ASN B 380 GLN B 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135807 restraints weight = 12200.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140115 restraints weight = 6769.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142962 restraints weight = 4730.066| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8675 Z= 0.152 Angle : 0.758 13.704 11816 Z= 0.366 Chirality : 0.046 0.263 1410 Planarity : 0.005 0.071 1458 Dihedral : 10.504 93.950 1380 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.17 % Favored : 96.57 % Rotamer: Outliers : 3.60 % Allowed : 31.36 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 1136 helix: 1.94 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -1.32 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 432 HIS 0.003 0.001 HIS B 310 PHE 0.026 0.002 PHE B 332 TYR 0.014 0.001 TYR A 104 ARG 0.002 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 2) link_NAG-ASN : angle 4.66596 ( 6) hydrogen bonds : bond 0.04359 ( 655) hydrogen bonds : angle 4.19055 ( 1959) covalent geometry : bond 0.00343 ( 8673) covalent geometry : angle 0.75129 (11810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.841 Fit side-chains REVERT: A 48 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8293 (tt0) REVERT: A 194 LYS cc_start: 0.8384 (tttt) cc_final: 0.7700 (tptt) REVERT: A 299 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: A 341 GLU cc_start: 0.7112 (pm20) cc_final: 0.6785 (pt0) REVERT: A 377 TYR cc_start: 0.7565 (m-80) cc_final: 0.7321 (m-80) REVERT: A 691 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7054 (tm-30) REVERT: B 365 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8292 (mm) REVERT: B 390 SER cc_start: 0.9003 (t) cc_final: 0.8121 (p) REVERT: B 394 LEU cc_start: 0.7717 (tp) cc_final: 0.7438 (tp) REVERT: B 413 MET cc_start: 0.6509 (tpp) cc_final: 0.6235 (ttt) REVERT: B 420 ILE cc_start: 0.8365 (tt) cc_final: 0.8064 (tp) REVERT: B 455 TYR cc_start: 0.7943 (m-80) cc_final: 0.7687 (m-80) outliers start: 28 outliers final: 22 residues processed: 188 average time/residue: 0.1786 time to fit residues: 48.3006 Evaluate side-chains 183 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 670 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.178912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137149 restraints weight = 12410.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141572 restraints weight = 6788.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144399 restraints weight = 4699.478| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8675 Z= 0.148 Angle : 0.779 14.889 11816 Z= 0.372 Chirality : 0.046 0.271 1410 Planarity : 0.005 0.072 1458 Dihedral : 10.091 90.281 1380 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.35 % Favored : 96.39 % Rotamer: Outliers : 3.21 % Allowed : 31.36 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 2.09 (0.26), residues: 1136 helix: 2.01 (0.17), residues: 914 sheet: None (None), residues: 0 loop : -1.30 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 432 HIS 0.002 0.001 HIS B 310 PHE 0.024 0.001 PHE B 332 TYR 0.011 0.001 TYR A 151 ARG 0.001 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 2) link_NAG-ASN : angle 4.82918 ( 6) hydrogen bonds : bond 0.04251 ( 655) hydrogen bonds : angle 4.13806 ( 1959) covalent geometry : bond 0.00332 ( 8673) covalent geometry : angle 0.77127 (11810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2782.16 seconds wall clock time: 49 minutes 29.35 seconds (2969.35 seconds total)