Starting phenix.real_space_refine on Sat Jun 7 05:04:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3z_61128/06_2025/9j3z_61128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3z_61128/06_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_61128/06_2025/9j3z_61128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3z_61128/06_2025/9j3z_61128.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3z_61128/06_2025/9j3z_61128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3z_61128/06_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-5710/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: 5.78, per 1000 atoms: 0.68 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: 2.19 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: 0.79 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: 2.49 Time building geometry restraints manager: 2.58 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: 1.170 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.630 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- 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 : 0.865 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: 0.1644 time to fit residues: 45.4149 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 : 0.830 ------------------------------------------------------------------------------- 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 = 54)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143698 restraints weight = 12462.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147722 restraints weight = 7077.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150323 restraints weight = 5039.957| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.846 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: 0.7707 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: A 381 ASN cc_start: 0.7226 (t0) cc_final: 0.6852 (t0) REVERT: B 130 ARG cc_start: 0.6832 (mtp180) cc_final: 0.6229 (ttm110) REVERT: B 216 GLN cc_start: 0.7760 (mt0) cc_final: 0.7557 (mt0) REVERT: B 296 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7097 (mm-30) REVERT: B 455 TYR cc_start: 0.7679 (m-80) cc_final: 0.7466 (m-80) outliers start: 27 outliers final: 11 residues processed: 207 average time/residue: 0.1843 time to fit residues: 53.8952 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 : 1.011 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 chunk 110 optimal weight: 30.0000 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** 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 = 0.4177 r_free = 0.4177 target = 0.183024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143207 restraints weight = 12608.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147386 restraints weight = 7094.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150043 restraints weight = 4997.827| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8675 Z= 0.138 Angle : 0.642 9.473 11816 Z= 0.321 Chirality : 0.043 0.188 1410 Planarity : 0.005 0.059 1458 Dihedral : 11.808 94.355 1382 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.38 % Favored : 97.36 % Rotamer: Outliers : 4.11 % Allowed : 25.58 % Favored : 70.31 % 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: 1.58 (0.25), residues: 1136 helix: 1.65 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -1.40 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.00765 ( 2) link_NAG-ASN : angle 4.64871 ( 6) hydrogen bonds : bond 0.04440 ( 655) hydrogen bonds : angle 4.00488 ( 1959) covalent geometry : bond 0.00297 ( 8673) covalent geometry : angle 0.63338 (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 226 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: A 377 TYR cc_start: 0.7105 (m-80) cc_final: 0.6840 (m-80) REVERT: A 381 ASN cc_start: 0.7125 (t0) cc_final: 0.6756 (t0) REVERT: B 130 ARG cc_start: 0.6890 (mtp180) cc_final: 0.6155 (ttm110) REVERT: B 296 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7090 (mm-30) REVERT: B 310 HIS cc_start: 0.8049 (p90) cc_final: 0.7811 (p90) REVERT: B 358 MET cc_start: 0.8053 (mmm) cc_final: 0.7744 (mtm) REVERT: B 390 SER cc_start: 0.8987 (t) cc_final: 0.8170 (p) REVERT: B 420 ILE cc_start: 0.8468 (tt) cc_final: 0.8237 (tp) REVERT: B 695 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.7035 (t80) outliers start: 32 outliers final: 18 residues processed: 210 average time/residue: 0.2130 time to fit residues: 63.6651 Evaluate side-chains 197 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 367 PHE Chi-restraints excluded: chain A residue 695 PHE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain B residue 73 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 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: 0.9990 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 30.0000 chunk 18 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.180985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.140326 restraints weight = 12606.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144303 restraints weight = 7168.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146818 restraints weight = 5148.885| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2773 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= 0.146 Angle : 0.653 9.909 11816 Z= 0.326 Chirality : 0.044 0.192 1410 Planarity : 0.004 0.064 1458 Dihedral : 11.410 91.537 1380 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.55 % Favored : 97.18 % Rotamer: Outliers : 4.76 % Allowed : 26.48 % Favored : 68.77 % 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: 1.91 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -1.34 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 432 HIS 0.007 0.001 HIS B 310 PHE 0.023 0.001 PHE B 221 TYR 0.017 0.001 TYR B 104 ARG 0.002 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00710 ( 2) link_NAG-ASN : angle 4.29269 ( 6) hydrogen bonds : bond 0.04200 ( 655) hydrogen bonds : angle 4.01002 ( 1959) covalent geometry : bond 0.00327 ( 8673) covalent geometry : angle 0.64632 (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: 37 poor density : 178 time to evaluate : 0.850 Fit side-chains REVERT: A 299 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: A 377 TYR cc_start: 0.7068 (m-80) cc_final: 0.6822 (m-80) REVERT: A 381 ASN cc_start: 0.7214 (t0) cc_final: 0.6911 (t0) REVERT: B 130 ARG cc_start: 0.6819 (mtp180) cc_final: 0.6113 (ttm110) REVERT: B 390 SER cc_start: 0.9021 (t) cc_final: 0.8190 (p) REVERT: B 413 MET cc_start: 0.7077 (tpp) cc_final: 0.6746 (tpp) REVERT: B 420 ILE cc_start: 0.8530 (tt) cc_final: 0.8286 (tp) REVERT: B 430 MET cc_start: 0.7902 (mmt) cc_final: 0.7584 (mmm) REVERT: B 455 TYR cc_start: 0.7691 (m-80) cc_final: 0.7371 (m-80) outliers start: 37 outliers final: 26 residues processed: 201 average time/residue: 0.1914 time to fit residues: 54.3493 Evaluate side-chains 190 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.8980 chunk 107 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.178046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136624 restraints weight = 12060.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140791 restraints weight = 6685.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143578 restraints weight = 4670.255| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8675 Z= 0.158 Angle : 0.678 10.412 11816 Z= 0.333 Chirality : 0.045 0.281 1410 Planarity : 0.004 0.071 1458 Dihedral : 11.191 90.994 1380 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.90 % Favored : 96.83 % Rotamer: Outliers : 5.91 % Allowed : 26.35 % Favored : 67.74 % 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: 2.07 (0.26), residues: 1136 helix: 2.01 (0.17), residues: 911 sheet: None (None), residues: 0 loop : -1.31 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 460 HIS 0.006 0.001 HIS B 310 PHE 0.023 0.002 PHE B 221 TYR 0.014 0.001 TYR B 104 ARG 0.003 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 2) link_NAG-ASN : angle 4.26422 ( 6) hydrogen bonds : bond 0.04281 ( 655) hydrogen bonds : angle 4.02923 ( 1959) covalent geometry : bond 0.00367 ( 8673) covalent geometry : angle 0.67121 (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 217 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8351 (tt0) REVERT: A 299 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: A 377 TYR cc_start: 0.7149 (m-80) cc_final: 0.6869 (m-80) REVERT: A 381 ASN cc_start: 0.7224 (t0) cc_final: 0.6941 (t0) REVERT: A 432 TRP cc_start: 0.7792 (t-100) cc_final: 0.7476 (t-100) REVERT: B 130 ARG cc_start: 0.6882 (mtp180) cc_final: 0.6078 (ttm110) REVERT: B 365 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8315 (mm) REVERT: B 390 SER cc_start: 0.8984 (t) cc_final: 0.8137 (p) REVERT: B 413 MET cc_start: 0.7008 (tpp) cc_final: 0.6645 (ttt) REVERT: B 420 ILE cc_start: 0.8592 (tt) cc_final: 0.8366 (tp) REVERT: B 430 MET cc_start: 0.7808 (mmt) cc_final: 0.7582 (mmm) REVERT: B 455 TYR cc_start: 0.7765 (m-80) cc_final: 0.7395 (m-80) outliers start: 46 outliers final: 28 residues processed: 203 average time/residue: 0.1796 time to fit residues: 51.7486 Evaluate side-chains 191 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 SER 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 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 395 ILE 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 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 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 400 ILE Chi-restraints excluded: chain B residue 450 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 380 GLN B 417 ASN B 703 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.179687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137821 restraints weight = 12038.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142199 restraints weight = 6651.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145003 restraints weight = 4637.198| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3286 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= 0.139 Angle : 0.675 11.391 11816 Z= 0.328 Chirality : 0.044 0.219 1410 Planarity : 0.004 0.073 1458 Dihedral : 10.910 90.399 1380 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.90 % Favored : 96.83 % Rotamer: Outliers : 4.37 % Allowed : 27.38 % Favored : 68.25 % 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: 911 sheet: None (None), residues: 0 loop : -1.28 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 460 HIS 0.006 0.001 HIS B 310 PHE 0.023 0.002 PHE B 332 TYR 0.012 0.001 TYR B 104 ARG 0.002 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 2) link_NAG-ASN : angle 4.09457 ( 6) hydrogen bonds : bond 0.04066 ( 655) hydrogen bonds : angle 3.95657 ( 1959) covalent geometry : bond 0.00312 ( 8673) covalent geometry : angle 0.66932 (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 215 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8333 (tt0) REVERT: A 185 PHE cc_start: 0.7626 (m-80) cc_final: 0.7219 (m-80) REVERT: A 194 LYS cc_start: 0.8487 (tttt) cc_final: 0.7734 (tptt) REVERT: A 299 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: A 377 TYR cc_start: 0.7213 (m-80) cc_final: 0.6928 (m-80) REVERT: A 381 ASN cc_start: 0.7166 (t0) cc_final: 0.6922 (t0) REVERT: A 432 TRP cc_start: 0.7829 (t-100) cc_final: 0.7543 (t-100) REVERT: B 89 ASN cc_start: 0.7283 (m110) cc_final: 0.7064 (m110) REVERT: B 130 ARG cc_start: 0.6872 (mtp180) cc_final: 0.6069 (ttm110) REVERT: B 296 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 390 SER cc_start: 0.8996 (t) cc_final: 0.8167 (p) REVERT: B 413 MET cc_start: 0.6941 (tpp) cc_final: 0.6659 (ttt) REVERT: B 420 ILE cc_start: 0.8488 (tt) cc_final: 0.8196 (tp) REVERT: B 430 MET cc_start: 0.7784 (mmt) cc_final: 0.7541 (mmm) REVERT: B 455 TYR cc_start: 0.7839 (m-80) cc_final: 0.7487 (m-80) outliers start: 34 outliers final: 23 residues processed: 201 average time/residue: 0.1746 time to fit residues: 50.0487 Evaluate side-chains 186 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL 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 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 292 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 B 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.180613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138904 restraints weight = 12094.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143348 restraints weight = 6618.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146149 restraints weight = 4579.438| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8675 Z= 0.135 Angle : 0.682 10.266 11816 Z= 0.330 Chirality : 0.044 0.198 1410 Planarity : 0.004 0.073 1458 Dihedral : 10.676 89.204 1380 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.90 % Favored : 96.83 % Rotamer: Outliers : 4.63 % Allowed : 28.79 % Favored : 66.58 % 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: 2.19 (0.26), residues: 1136 helix: 2.08 (0.17), residues: 913 sheet: None (None), residues: 0 loop : -1.24 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 460 HIS 0.008 0.002 HIS A 716 PHE 0.021 0.001 PHE B 221 TYR 0.014 0.001 TYR B 104 ARG 0.002 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 2) link_NAG-ASN : angle 4.16757 ( 6) hydrogen bonds : bond 0.03986 ( 655) hydrogen bonds : angle 3.91218 ( 1959) covalent geometry : bond 0.00300 ( 8673) covalent geometry : angle 0.67559 (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 212 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8297 (tt0) REVERT: A 185 PHE cc_start: 0.7583 (m-80) cc_final: 0.7333 (m-80) REVERT: A 194 LYS cc_start: 0.8468 (tttt) cc_final: 0.7726 (tptt) REVERT: A 299 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: A 377 TYR cc_start: 0.7214 (m-80) cc_final: 0.6930 (m-80) REVERT: A 381 ASN cc_start: 0.7123 (t0) cc_final: 0.6864 (t0) REVERT: A 432 TRP cc_start: 0.7818 (t-100) cc_final: 0.7562 (t-100) REVERT: B 89 ASN cc_start: 0.7296 (m110) cc_final: 0.7056 (m110) REVERT: B 130 ARG cc_start: 0.6860 (mtp180) cc_final: 0.6080 (ttm110) REVERT: B 365 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8218 (mm) REVERT: B 390 SER cc_start: 0.8990 (t) cc_final: 0.8151 (p) REVERT: B 413 MET cc_start: 0.6658 (tpp) cc_final: 0.6379 (ttt) REVERT: B 420 ILE cc_start: 0.8496 (tt) cc_final: 0.8185 (tp) REVERT: B 430 MET cc_start: 0.7786 (mmt) cc_final: 0.7524 (mmm) REVERT: B 455 TYR cc_start: 0.7739 (m-80) cc_final: 0.7378 (m-80) outliers start: 36 outliers final: 27 residues processed: 197 average time/residue: 0.1771 time to fit residues: 49.8984 Evaluate side-chains 202 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 155 GLU 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 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 181 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 103 optimal weight: 50.0000 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.180267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138637 restraints weight = 12241.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143011 restraints weight = 6743.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.145825 restraints weight = 4705.223| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8675 Z= 0.138 Angle : 0.696 14.264 11816 Z= 0.336 Chirality : 0.045 0.365 1410 Planarity : 0.004 0.073 1458 Dihedral : 10.568 89.066 1380 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.90 % Favored : 96.83 % Rotamer: Outliers : 5.40 % Allowed : 28.53 % Favored : 66.07 % 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: 2.19 (0.26), residues: 1136 helix: 2.08 (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 0.017 0.001 TRP A 460 HIS 0.008 0.002 HIS A 716 PHE 0.021 0.001 PHE B 221 TYR 0.019 0.001 TYR A 104 ARG 0.001 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 2) link_NAG-ASN : angle 4.24062 ( 6) hydrogen bonds : bond 0.03993 ( 655) hydrogen bonds : angle 3.93421 ( 1959) covalent geometry : bond 0.00314 ( 8673) covalent geometry : angle 0.68998 (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 215 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8304 (tt0) REVERT: A 185 PHE cc_start: 0.7590 (m-80) cc_final: 0.7344 (m-80) REVERT: A 270 ARG cc_start: 0.2513 (mpt-90) cc_final: 0.2013 (mtt180) REVERT: A 299 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: A 377 TYR cc_start: 0.7241 (m-80) cc_final: 0.6956 (m-80) REVERT: A 381 ASN cc_start: 0.7127 (t0) cc_final: 0.6869 (t0) REVERT: A 432 TRP cc_start: 0.7842 (t-100) cc_final: 0.7605 (t-100) REVERT: B 130 ARG cc_start: 0.6849 (mtp180) cc_final: 0.6068 (ttm110) REVERT: B 365 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8229 (mm) REVERT: B 390 SER cc_start: 0.8980 (t) cc_final: 0.8113 (p) REVERT: B 394 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7397 (tp) REVERT: B 413 MET cc_start: 0.6637 (tpp) cc_final: 0.6382 (ttt) REVERT: B 420 ILE cc_start: 0.8433 (tt) cc_final: 0.8130 (tp) REVERT: B 455 TYR cc_start: 0.7843 (m-80) cc_final: 0.7534 (m-80) outliers start: 42 outliers final: 29 residues processed: 197 average time/residue: 0.1790 time to fit residues: 51.0720 Evaluate side-chains 197 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 155 GLU 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 292 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 HIS 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 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 181 ASN 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 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 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: 6.9990 chunk 105 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 46 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** A 716 HIS B 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.173080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130315 restraints weight = 12384.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134611 restraints weight = 6935.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137318 restraints weight = 4874.236| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8675 Z= 0.247 Angle : 0.827 12.908 11816 Z= 0.401 Chirality : 0.050 0.358 1410 Planarity : 0.005 0.072 1458 Dihedral : 10.927 97.605 1380 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.48 % Rotamer: Outliers : 4.37 % Allowed : 29.56 % Favored : 66.07 % 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: 1.89 (0.26), residues: 1136 helix: 1.86 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -1.33 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 460 HIS 0.010 0.003 HIS A 716 PHE 0.025 0.002 PHE B 332 TYR 0.019 0.002 TYR A 104 ARG 0.003 0.000 ARG A 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 2) link_NAG-ASN : angle 4.36770 ( 6) hydrogen bonds : bond 0.04955 ( 655) hydrogen bonds : angle 4.32022 ( 1959) covalent geometry : bond 0.00600 ( 8673) covalent geometry : angle 0.82142 (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 197 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.851 Fit side-chains REVERT: A 48 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8405 (tt0) REVERT: A 185 PHE cc_start: 0.7927 (m-80) cc_final: 0.7599 (m-80) REVERT: A 194 LYS cc_start: 0.8480 (tttt) cc_final: 0.7650 (tptt) REVERT: A 299 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: A 377 TYR cc_start: 0.7600 (m-80) cc_final: 0.7343 (m-80) REVERT: A 701 PHE cc_start: 0.7331 (m-80) cc_final: 0.7068 (m-80) REVERT: B 130 ARG cc_start: 0.6938 (mtp180) cc_final: 0.6038 (ttm110) REVERT: B 365 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 413 MET cc_start: 0.6627 (tpp) cc_final: 0.6393 (ttt) REVERT: B 420 ILE cc_start: 0.8580 (tt) cc_final: 0.8302 (tp) REVERT: B 455 TYR cc_start: 0.7843 (m-80) cc_final: 0.7470 (m-80) outliers start: 34 outliers final: 25 residues processed: 183 average time/residue: 0.2045 time to fit residues: 54.5946 Evaluate side-chains 184 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 157 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 310 HIS 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 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 93 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 ASN 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 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 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: 0.9990 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** A 716 HIS B 181 ASN B 216 GLN B 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135380 restraints weight = 12178.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139701 restraints weight = 6798.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142414 restraints weight = 4765.304| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8675 Z= 0.157 Angle : 0.743 12.776 11816 Z= 0.360 Chirality : 0.046 0.321 1410 Planarity : 0.005 0.073 1458 Dihedral : 10.320 92.977 1380 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.43 % Favored : 96.30 % Rotamer: Outliers : 3.73 % Allowed : 30.72 % Favored : 65.55 % 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: 2.10 (0.26), residues: 1136 helix: 2.01 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -1.23 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 432 HIS 0.010 0.003 HIS A 716 PHE 0.023 0.002 PHE B 221 TYR 0.019 0.001 TYR A 104 ARG 0.001 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 2) link_NAG-ASN : angle 4.63252 ( 6) hydrogen bonds : bond 0.04284 ( 655) hydrogen bonds : angle 4.12790 ( 1959) covalent geometry : bond 0.00363 ( 8673) covalent geometry : angle 0.73617 (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 197 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8309 (tt0) REVERT: A 185 PHE cc_start: 0.7698 (m-80) cc_final: 0.7438 (m-80) REVERT: A 194 LYS cc_start: 0.8387 (tttt) cc_final: 0.7705 (tptt) REVERT: A 299 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: A 377 TYR cc_start: 0.7511 (m-80) cc_final: 0.7253 (m-80) REVERT: B 130 ARG cc_start: 0.6860 (mtp180) cc_final: 0.5964 (ttm110) REVERT: B 365 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8274 (mm) REVERT: B 390 SER cc_start: 0.8840 (t) cc_final: 0.7986 (p) REVERT: B 394 LEU cc_start: 0.7776 (tp) cc_final: 0.7495 (tp) REVERT: B 413 MET cc_start: 0.6517 (tpp) cc_final: 0.6293 (ttt) REVERT: B 420 ILE cc_start: 0.8364 (tt) cc_final: 0.8059 (tp) REVERT: B 455 TYR cc_start: 0.7968 (m-80) cc_final: 0.7665 (m-80) outliers start: 29 outliers final: 23 residues processed: 185 average time/residue: 0.2312 time to fit residues: 62.7722 Evaluate side-chains 183 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 310 HIS Chi-restraints excluded: chain A residue 340 VAL 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 A residue 716 HIS 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 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 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: 0.9990 chunk 2 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.178010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136369 restraints weight = 12472.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140834 restraints weight = 6847.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143530 restraints weight = 4738.390| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8675 Z= 0.154 Angle : 0.771 12.085 11816 Z= 0.369 Chirality : 0.046 0.304 1410 Planarity : 0.005 0.074 1458 Dihedral : 10.016 90.942 1380 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.52 % Favored : 96.21 % Rotamer: Outliers : 3.60 % Allowed : 30.98 % 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: 2.13 (0.26), residues: 1136 helix: 2.04 (0.17), residues: 914 sheet: None (None), residues: 0 loop : -1.31 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 432 HIS 0.008 0.002 HIS A 716 PHE 0.023 0.001 PHE B 221 TYR 0.019 0.001 TYR A 689 ARG 0.002 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 2) link_NAG-ASN : angle 4.79803 ( 6) hydrogen bonds : bond 0.04231 ( 655) hydrogen bonds : angle 4.07559 ( 1959) covalent geometry : bond 0.00354 ( 8673) covalent geometry : angle 0.76401 (11810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3711.79 seconds wall clock time: 68 minutes 7.89 seconds (4087.89 seconds total)