Starting phenix.real_space_refine on Wed Mar 4 09:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kuk_9578/03_2026/6kuk_9578_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kuk_9578/03_2026/6kuk_9578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kuk_9578/03_2026/6kuk_9578_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kuk_9578/03_2026/6kuk_9578_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kuk_9578/03_2026/6kuk_9578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kuk_9578/03_2026/6kuk_9578.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 23 5.49 5 S 109 5.16 5 C 7695 2.51 5 N 2091 2.21 5 O 2326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12244 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4176 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5568 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 5} Chain: "V" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 2.34, per 1000 atoms: 0.19 Number of scatterers: 12244 At special positions: 0 Unit cell: (111.52, 110.16, 110.16, 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 109 16.00 P 23 15.00 O 2326 8.00 N 2091 7.00 C 7695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 576.4 milliseconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 47.5% alpha, 7.8% beta 7 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.774A pdb=" N ALA A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.661A pdb=" N THR A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.103A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.710A pdb=" N PHE A 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.577A pdb=" N ASP A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.719A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 589 removed outlier: 3.758A pdb=" N MET A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.831A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 684 through 703 Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.838A pdb=" N LEU B 7 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.843A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.909A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 104 through 118 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.658A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.944A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.579A pdb=" N GLU B 313 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS B 314 " --> pdb=" O TRP B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 314' Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.822A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.605A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 382' Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.705A pdb=" N ARG B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 425 removed outlier: 3.539A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.711A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.717A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.741A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 3.574A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.577A pdb=" N THR C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 37 removed outlier: 4.001A pdb=" N THR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.720A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.726A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.690A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 removed outlier: 4.391A pdb=" N GLU C 178 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 179 " --> pdb=" O GLU C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 179' Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 215 removed outlier: 4.078A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 238 through 243 removed outlier: 4.085A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.690A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 478 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 353 removed outlier: 5.656A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 466 removed outlier: 6.533A pdb=" N LYS A 544 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR A 525 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 546 " --> pdb=" O ALA A 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.680A pdb=" N ILE B 226 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB2, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.706A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 149 through 153 506 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3496 1.33 - 1.46: 2456 1.46 - 1.58: 6357 1.58 - 1.70: 44 1.70 - 1.82: 181 Bond restraints: 12534 Sorted by residual: bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.27e-02 6.20e+03 2.41e+01 bond pdb=" N ILE B 731 " pdb=" CA ILE B 731 " ideal model delta sigma weight residual 1.459 1.423 0.036 1.25e-02 6.40e+03 8.35e+00 bond pdb=" N ILE B 730 " pdb=" CA ILE B 730 " ideal model delta sigma weight residual 1.459 1.430 0.029 1.25e-02 6.40e+03 5.24e+00 bond pdb=" C LEU B 510 " pdb=" N PRO B 511 " ideal model delta sigma weight residual 1.337 1.357 -0.021 1.11e-02 8.12e+03 3.55e+00 bond pdb=" CG1 ILE A 447 " pdb=" CD1 ILE A 447 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.24e+00 ... (remaining 12529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 16135 2.14 - 4.28: 709 4.28 - 6.43: 75 6.43 - 8.57: 24 8.57 - 10.71: 5 Bond angle restraints: 16948 Sorted by residual: angle pdb=" N ILE B 393 " pdb=" CA ILE B 393 " pdb=" C ILE B 393 " ideal model delta sigma weight residual 113.20 105.82 7.38 9.60e-01 1.09e+00 5.90e+01 angle pdb=" CA LYS A 488 " pdb=" CB LYS A 488 " pdb=" CG LYS A 488 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.92e+01 angle pdb=" N GLY B 441 " pdb=" CA GLY B 441 " pdb=" C GLY B 441 " ideal model delta sigma weight residual 110.58 116.42 -5.84 1.35e+00 5.49e-01 1.87e+01 angle pdb=" O ILE B 730 " pdb=" C ILE B 730 " pdb=" N ILE B 731 " ideal model delta sigma weight residual 122.57 127.75 -5.18 1.25e+00 6.40e-01 1.72e+01 angle pdb=" C THR B 515 " pdb=" CA THR B 515 " pdb=" CB THR B 515 " ideal model delta sigma weight residual 110.44 104.10 6.34 1.68e+00 3.54e-01 1.42e+01 ... (remaining 16943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 7170 15.63 - 31.26: 391 31.26 - 46.89: 102 46.89 - 62.51: 27 62.51 - 78.14: 25 Dihedral angle restraints: 7715 sinusoidal: 3455 harmonic: 4260 Sorted by residual: dihedral pdb=" CA ILE C 186 " pdb=" C ILE C 186 " pdb=" N GLN C 187 " pdb=" CA GLN C 187 " ideal model delta harmonic sigma weight residual 180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASN B 728 " pdb=" C ASN B 728 " pdb=" N GLY B 729 " pdb=" CA GLY B 729 " ideal model delta harmonic sigma weight residual -180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ILE A 604 " pdb=" C ILE A 604 " pdb=" N ALA A 605 " pdb=" CA ALA A 605 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 7712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1476 0.072 - 0.143: 347 0.143 - 0.214: 28 0.214 - 0.286: 3 0.286 - 0.357: 1 Chirality restraints: 1855 Sorted by residual: chirality pdb=" CB ILE B 304 " pdb=" CA ILE B 304 " pdb=" CG1 ILE B 304 " pdb=" CG2 ILE B 304 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB ILE B 72 " pdb=" CA ILE B 72 " pdb=" CG1 ILE B 72 " pdb=" CG2 ILE B 72 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE C 249 " pdb=" CA ILE C 249 " pdb=" CG1 ILE C 249 " pdb=" CG2 ILE C 249 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1852 not shown) Planarity restraints: 2068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 386 " -0.020 2.00e-02 2.50e+03 1.70e-02 7.19e+00 pdb=" CG TRP A 386 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 386 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 386 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 386 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 386 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 386 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 386 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 386 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 386 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 155 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO C 156 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 731 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ILE B 731 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE B 731 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 732 " 0.013 2.00e-02 2.50e+03 ... (remaining 2065 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1419 2.74 - 3.28: 11176 3.28 - 3.82: 18742 3.82 - 4.36: 22829 4.36 - 4.90: 38857 Nonbonded interactions: 93023 Sorted by model distance: nonbonded pdb=" OE2 GLU A 408 " pdb=" NH2 ARG B 557 " model vdw 2.201 3.120 nonbonded pdb=" OH TYR B 49 " pdb=" NZ LYS B 310 " model vdw 2.221 3.120 nonbonded pdb=" OD2 ASP B 615 " pdb=" NZ LYS C 129 " model vdw 2.235 3.120 nonbonded pdb=" O ALA B 152 " pdb=" OG1 THR B 156 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN A 649 " pdb=" OH TYR B 6 " model vdw 2.269 3.040 ... (remaining 93018 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 0.370 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 : 0.008 0.074 12534 Z= 0.352 Angle : 1.025 10.708 16948 Z= 0.565 Chirality : 0.059 0.357 1855 Planarity : 0.007 0.061 2068 Dihedral : 11.980 78.142 4949 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.61 % Favored : 91.19 % Rotamer: Outliers : 0.47 % Allowed : 3.04 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.88 (0.16), residues: 1441 helix: -3.38 (0.12), residues: 646 sheet: -2.14 (0.46), residues: 126 loop : -3.25 (0.19), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 573 TYR 0.033 0.003 TYR B 38 PHE 0.033 0.004 PHE B 122 TRP 0.044 0.004 TRP A 386 HIS 0.012 0.003 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00790 (12534) covalent geometry : angle 1.02507 (16948) hydrogen bonds : bond 0.16545 ( 525) hydrogen bonds : angle 9.11073 ( 1448) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 450 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LYS cc_start: 0.8425 (tmmt) cc_final: 0.7937 (tmmt) REVERT: A 277 HIS cc_start: 0.6382 (t70) cc_final: 0.6098 (t-90) REVERT: A 278 ASP cc_start: 0.7021 (t0) cc_final: 0.6750 (t0) REVERT: A 290 ASP cc_start: 0.7697 (m-30) cc_final: 0.7345 (m-30) REVERT: A 364 GLU cc_start: 0.7887 (mp0) cc_final: 0.7495 (mp0) REVERT: A 367 GLN cc_start: 0.6979 (pt0) cc_final: 0.6773 (mt0) REVERT: A 495 ASP cc_start: 0.7719 (m-30) cc_final: 0.7335 (p0) REVERT: A 650 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7694 (pttp) REVERT: B 47 TYR cc_start: 0.8098 (m-10) cc_final: 0.7857 (m-10) REVERT: B 140 MET cc_start: 0.7415 (mtt) cc_final: 0.7013 (mtt) REVERT: B 147 GLN cc_start: 0.8496 (tp-100) cc_final: 0.7534 (tm-30) REVERT: B 182 LYS cc_start: 0.7447 (mtmt) cc_final: 0.6931 (mtmm) REVERT: B 490 LEU cc_start: 0.8707 (tp) cc_final: 0.8451 (tp) REVERT: B 515 THR cc_start: 0.6793 (p) cc_final: 0.6547 (t) REVERT: B 560 TYR cc_start: 0.7238 (m-80) cc_final: 0.6870 (m-80) REVERT: B 578 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.5185 (mtp180) REVERT: B 685 TYR cc_start: 0.7534 (m-10) cc_final: 0.6901 (m-80) REVERT: C 18 LYS cc_start: 0.7200 (mttt) cc_final: 0.6863 (tppt) REVERT: C 65 ARG cc_start: 0.7065 (ttt90) cc_final: 0.6785 (ttm-80) REVERT: C 80 ILE cc_start: 0.5637 (mt) cc_final: 0.4733 (mt) REVERT: C 213 MET cc_start: 0.5011 (ptm) cc_final: 0.4581 (ptm) outliers start: 6 outliers final: 1 residues processed: 454 average time/residue: 0.1301 time to fit residues: 80.5103 Evaluate side-chains 293 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 578 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN A 640 ASN A 647 ASN B 84 ASN B 147 GLN B 154 GLN B 303 ASN B 312 ASN B 477 ASN C 148 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.177025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.147222 restraints weight = 18073.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150361 restraints weight = 11089.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152436 restraints weight = 7898.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153786 restraints weight = 6288.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.154700 restraints weight = 5427.344| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12534 Z= 0.135 Angle : 0.662 16.738 16948 Z= 0.339 Chirality : 0.042 0.179 1855 Planarity : 0.005 0.056 2068 Dihedral : 11.721 73.864 1930 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 3.04 % Allowed : 9.82 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.19), residues: 1441 helix: -1.22 (0.18), residues: 657 sheet: -1.38 (0.50), residues: 115 loop : -2.91 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 131 TYR 0.014 0.001 TYR B 692 PHE 0.028 0.001 PHE B 108 TRP 0.018 0.001 TRP A 386 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00285 (12534) covalent geometry : angle 0.66197 (16948) hydrogen bonds : bond 0.05120 ( 525) hydrogen bonds : angle 5.38391 ( 1448) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 343 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8055 (pt) REVERT: A 231 ASP cc_start: 0.8667 (t70) cc_final: 0.8234 (t70) REVERT: A 277 HIS cc_start: 0.6425 (t70) cc_final: 0.6204 (t-90) REVERT: A 290 ASP cc_start: 0.7464 (m-30) cc_final: 0.7260 (m-30) REVERT: A 292 PHE cc_start: 0.6811 (t80) cc_final: 0.6608 (t80) REVERT: A 318 LEU cc_start: 0.8833 (tp) cc_final: 0.8594 (tp) REVERT: A 367 GLN cc_start: 0.6944 (pt0) cc_final: 0.6734 (mt0) REVERT: A 416 MET cc_start: 0.8657 (ppp) cc_final: 0.7961 (ppp) REVERT: A 442 LYS cc_start: 0.8992 (tttt) cc_final: 0.8654 (tttm) REVERT: A 633 TYR cc_start: 0.8997 (m-80) cc_final: 0.8786 (m-80) REVERT: A 653 LEU cc_start: 0.8841 (mm) cc_final: 0.8585 (mt) REVERT: B 98 GLU cc_start: 0.6671 (tp30) cc_final: 0.6410 (tp30) REVERT: B 147 GLN cc_start: 0.8701 (tp40) cc_final: 0.7590 (tm-30) REVERT: B 182 LYS cc_start: 0.7311 (mtmt) cc_final: 0.6948 (mtmm) REVERT: B 259 THR cc_start: 0.8321 (p) cc_final: 0.8108 (t) REVERT: B 262 GLN cc_start: 0.8409 (tt0) cc_final: 0.7995 (tm-30) REVERT: B 423 MET cc_start: 0.8543 (mtm) cc_final: 0.8322 (mtp) REVERT: B 515 THR cc_start: 0.6640 (p) cc_final: 0.6339 (t) REVERT: B 560 TYR cc_start: 0.7282 (m-80) cc_final: 0.6878 (m-80) REVERT: B 685 TYR cc_start: 0.7656 (m-10) cc_final: 0.7317 (m-80) REVERT: C 18 LYS cc_start: 0.7281 (mttt) cc_final: 0.6695 (tppt) REVERT: C 51 MET cc_start: 0.7340 (tpp) cc_final: 0.6458 (tpp) REVERT: C 129 LYS cc_start: 0.7160 (tmtt) cc_final: 0.6653 (tptt) REVERT: C 213 MET cc_start: 0.5398 (ptm) cc_final: 0.4985 (ptm) REVERT: C 228 PHE cc_start: 0.7779 (p90) cc_final: 0.7549 (p90) outliers start: 39 outliers final: 23 residues processed: 362 average time/residue: 0.1122 time to fit residues: 58.0271 Evaluate side-chains 303 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.170634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141496 restraints weight = 18672.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144459 restraints weight = 11409.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146448 restraints weight = 8155.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147532 restraints weight = 6515.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.148514 restraints weight = 5676.484| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12534 Z= 0.192 Angle : 0.688 16.146 16948 Z= 0.350 Chirality : 0.045 0.160 1855 Planarity : 0.005 0.051 2068 Dihedral : 11.553 73.701 1926 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 3.66 % Allowed : 12.47 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.20), residues: 1441 helix: -0.53 (0.19), residues: 668 sheet: -1.36 (0.50), residues: 119 loop : -2.69 (0.21), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 220 TYR 0.023 0.002 TYR B 320 PHE 0.021 0.002 PHE B 108 TRP 0.017 0.002 TRP A 386 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00432 (12534) covalent geometry : angle 0.68812 (16948) hydrogen bonds : bond 0.05277 ( 525) hydrogen bonds : angle 5.08047 ( 1448) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8573 (t70) cc_final: 0.8153 (t70) REVERT: A 290 ASP cc_start: 0.7531 (m-30) cc_final: 0.7246 (m-30) REVERT: A 353 GLN cc_start: 0.7117 (mp10) cc_final: 0.6741 (mp10) REVERT: A 367 GLN cc_start: 0.6995 (pt0) cc_final: 0.6790 (mt0) REVERT: A 653 LEU cc_start: 0.8942 (mm) cc_final: 0.8677 (mt) REVERT: B 165 MET cc_start: 0.7444 (mmm) cc_final: 0.7180 (mmm) REVERT: B 182 LYS cc_start: 0.7135 (mtmt) cc_final: 0.6683 (mttp) REVERT: B 423 MET cc_start: 0.8715 (mtm) cc_final: 0.8423 (mtp) REVERT: B 442 LEU cc_start: 0.8558 (tp) cc_final: 0.8343 (tp) REVERT: B 515 THR cc_start: 0.6690 (p) cc_final: 0.6328 (t) REVERT: B 560 TYR cc_start: 0.7346 (m-80) cc_final: 0.6872 (m-80) REVERT: C 18 LYS cc_start: 0.7673 (mttt) cc_final: 0.7025 (tppt) REVERT: C 51 MET cc_start: 0.7406 (tpp) cc_final: 0.6582 (tpp) REVERT: C 213 MET cc_start: 0.5467 (ptm) cc_final: 0.5025 (ptm) outliers start: 47 outliers final: 32 residues processed: 307 average time/residue: 0.1067 time to fit residues: 47.2654 Evaluate side-chains 288 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.2980 chunk 130 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 303 ASN C 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.173218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143972 restraints weight = 18359.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146925 restraints weight = 11334.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.148854 restraints weight = 8130.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.150142 restraints weight = 6548.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150811 restraints weight = 5662.655| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12534 Z= 0.146 Angle : 0.645 16.797 16948 Z= 0.326 Chirality : 0.043 0.206 1855 Planarity : 0.004 0.045 2068 Dihedral : 11.409 73.684 1926 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 3.43 % Allowed : 14.19 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.21), residues: 1441 helix: -0.17 (0.19), residues: 675 sheet: -1.26 (0.50), residues: 119 loop : -2.59 (0.21), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.010 0.001 TYR B 320 PHE 0.018 0.001 PHE B 108 TRP 0.015 0.001 TRP A 386 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00331 (12534) covalent geometry : angle 0.64546 (16948) hydrogen bonds : bond 0.04665 ( 525) hydrogen bonds : angle 4.84042 ( 1448) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8502 (t70) cc_final: 0.8051 (t70) REVERT: A 353 GLN cc_start: 0.7084 (mp10) cc_final: 0.6713 (mp10) REVERT: A 367 GLN cc_start: 0.7045 (pt0) cc_final: 0.6719 (mt0) REVERT: A 650 LYS cc_start: 0.8121 (ptpp) cc_final: 0.7788 (ptpp) REVERT: A 653 LEU cc_start: 0.8863 (mm) cc_final: 0.8598 (mt) REVERT: B 1 MET cc_start: 0.8400 (tmm) cc_final: 0.8196 (tmm) REVERT: B 95 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6259 (mm-30) REVERT: B 147 GLN cc_start: 0.8828 (tp40) cc_final: 0.8586 (tp-100) REVERT: B 151 ASP cc_start: 0.7231 (m-30) cc_final: 0.6881 (m-30) REVERT: B 165 MET cc_start: 0.7526 (mmm) cc_final: 0.7144 (mmm) REVERT: B 222 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7537 (mmm-85) REVERT: B 423 MET cc_start: 0.8652 (mtm) cc_final: 0.8312 (mtp) REVERT: B 515 THR cc_start: 0.6731 (p) cc_final: 0.6457 (t) REVERT: B 560 TYR cc_start: 0.7266 (m-80) cc_final: 0.6793 (m-80) REVERT: C 18 LYS cc_start: 0.7646 (mttt) cc_final: 0.6998 (tppt) REVERT: C 51 MET cc_start: 0.7349 (tpp) cc_final: 0.6341 (tpp) REVERT: C 55 MET cc_start: 0.4650 (mmp) cc_final: 0.4158 (mmm) REVERT: C 65 ARG cc_start: 0.7422 (ttt90) cc_final: 0.7081 (ttm-80) REVERT: C 171 MET cc_start: 0.8134 (mmm) cc_final: 0.7368 (mtm) REVERT: C 213 MET cc_start: 0.5438 (ptm) cc_final: 0.4999 (ptm) outliers start: 44 outliers final: 31 residues processed: 300 average time/residue: 0.1081 time to fit residues: 46.6083 Evaluate side-chains 277 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 82 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.167192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137589 restraints weight = 18763.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140352 restraints weight = 11715.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142212 restraints weight = 8543.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143333 restraints weight = 6919.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144158 restraints weight = 6062.742| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12534 Z= 0.241 Angle : 0.733 16.910 16948 Z= 0.374 Chirality : 0.046 0.163 1855 Planarity : 0.005 0.045 2068 Dihedral : 11.512 73.417 1926 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.67 % Favored : 91.26 % Rotamer: Outliers : 4.29 % Allowed : 15.12 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.21), residues: 1441 helix: -0.29 (0.19), residues: 676 sheet: -1.40 (0.48), residues: 124 loop : -2.67 (0.21), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 222 TYR 0.015 0.002 TYR A 633 PHE 0.027 0.002 PHE B 122 TRP 0.019 0.002 TRP A 386 HIS 0.007 0.002 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00556 (12534) covalent geometry : angle 0.73324 (16948) hydrogen bonds : bond 0.05554 ( 525) hydrogen bonds : angle 5.14582 ( 1448) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 263 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8470 (t70) cc_final: 0.7953 (t70) REVERT: A 235 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.8174 (tpp-160) REVERT: A 332 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 426 GLU cc_start: 0.8058 (tp30) cc_final: 0.7751 (tm-30) REVERT: A 653 LEU cc_start: 0.9062 (mm) cc_final: 0.8832 (mt) REVERT: B 1 MET cc_start: 0.8386 (tmm) cc_final: 0.8183 (tmm) REVERT: B 55 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7367 (pm20) REVERT: B 95 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6499 (mm-30) REVERT: B 151 ASP cc_start: 0.7175 (m-30) cc_final: 0.6922 (m-30) REVERT: B 222 ARG cc_start: 0.7787 (ttm170) cc_final: 0.7474 (mmm-85) REVERT: B 515 THR cc_start: 0.7186 (p) cc_final: 0.6885 (t) REVERT: B 560 TYR cc_start: 0.7439 (m-80) cc_final: 0.6863 (m-80) REVERT: C 18 LYS cc_start: 0.7932 (mttt) cc_final: 0.7066 (tppt) REVERT: C 38 TRP cc_start: 0.7101 (OUTLIER) cc_final: 0.6406 (m100) REVERT: C 51 MET cc_start: 0.7487 (tpp) cc_final: 0.6518 (tpp) REVERT: C 65 ARG cc_start: 0.7750 (ttt90) cc_final: 0.7404 (ttm-80) REVERT: C 94 MET cc_start: 0.2104 (mmp) cc_final: 0.1355 (mmm) REVERT: C 171 MET cc_start: 0.8256 (mmm) cc_final: 0.7558 (mtm) REVERT: C 213 MET cc_start: 0.5442 (ptm) cc_final: 0.5003 (ptm) REVERT: C 232 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7839 (mtm-85) outliers start: 55 outliers final: 43 residues processed: 299 average time/residue: 0.1059 time to fit residues: 45.8802 Evaluate side-chains 288 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 100 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 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 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.172044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142836 restraints weight = 18601.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145746 restraints weight = 11618.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147579 restraints weight = 8381.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148693 restraints weight = 6758.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149503 restraints weight = 5882.320| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12534 Z= 0.131 Angle : 0.625 17.480 16948 Z= 0.314 Chirality : 0.042 0.158 1855 Planarity : 0.004 0.050 2068 Dihedral : 11.297 73.601 1926 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 2.96 % Allowed : 17.54 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.21), residues: 1441 helix: 0.09 (0.20), residues: 682 sheet: -0.66 (0.52), residues: 108 loop : -2.57 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 131 TYR 0.012 0.001 TYR B 560 PHE 0.017 0.001 PHE B 108 TRP 0.016 0.001 TRP A 386 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00300 (12534) covalent geometry : angle 0.62527 (16948) hydrogen bonds : bond 0.04375 ( 525) hydrogen bonds : angle 4.79007 ( 1448) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8288 (t70) cc_final: 0.7929 (t70) REVERT: A 356 LYS cc_start: 0.7851 (mptt) cc_final: 0.7540 (mmtm) REVERT: A 426 GLU cc_start: 0.8062 (tp30) cc_final: 0.7617 (tm-30) REVERT: A 497 MET cc_start: 0.6806 (mmm) cc_final: 0.6468 (mmp) REVERT: A 650 LYS cc_start: 0.7941 (ptpp) cc_final: 0.7585 (ptpp) REVERT: A 653 LEU cc_start: 0.8889 (mm) cc_final: 0.8585 (mt) REVERT: B 1 MET cc_start: 0.8431 (tmm) cc_final: 0.8192 (tmm) REVERT: B 47 TYR cc_start: 0.8216 (m-10) cc_final: 0.7927 (m-10) REVERT: B 55 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7301 (pm20) REVERT: B 95 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6694 (mm-30) REVERT: B 98 GLU cc_start: 0.7187 (tp30) cc_final: 0.6748 (tm-30) REVERT: B 151 ASP cc_start: 0.7122 (m-30) cc_final: 0.6788 (m-30) REVERT: B 182 LYS cc_start: 0.7009 (mttp) cc_final: 0.6545 (mtmm) REVERT: B 222 ARG cc_start: 0.7661 (ttm170) cc_final: 0.7287 (mmm-85) REVERT: B 382 MET cc_start: 0.7119 (mtp) cc_final: 0.6865 (ttm) REVERT: B 560 TYR cc_start: 0.7296 (m-80) cc_final: 0.6775 (m-80) REVERT: B 587 LYS cc_start: 0.7442 (mttt) cc_final: 0.6968 (mttt) REVERT: C 18 LYS cc_start: 0.7886 (mttt) cc_final: 0.7060 (tppt) REVERT: C 51 MET cc_start: 0.7759 (tpp) cc_final: 0.7121 (tpp) REVERT: C 65 ARG cc_start: 0.7747 (ttt90) cc_final: 0.7344 (ttm-80) REVERT: C 171 MET cc_start: 0.8106 (mmm) cc_final: 0.7395 (mtm) REVERT: C 213 MET cc_start: 0.5508 (ptm) cc_final: 0.5081 (ptm) outliers start: 38 outliers final: 28 residues processed: 287 average time/residue: 0.1071 time to fit residues: 44.3143 Evaluate side-chains 281 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 106 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139940 restraints weight = 18424.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142720 restraints weight = 11427.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144264 restraints weight = 8268.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145652 restraints weight = 6765.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145893 restraints weight = 5879.113| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12534 Z= 0.177 Angle : 0.672 17.528 16948 Z= 0.337 Chirality : 0.044 0.154 1855 Planarity : 0.004 0.053 2068 Dihedral : 11.342 73.499 1926 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 3.35 % Allowed : 18.71 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.21), residues: 1441 helix: 0.17 (0.20), residues: 672 sheet: -0.71 (0.52), residues: 108 loop : -2.51 (0.21), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 131 TYR 0.008 0.001 TYR A 208 PHE 0.020 0.002 PHE B 122 TRP 0.014 0.002 TRP A 386 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00411 (12534) covalent geometry : angle 0.67165 (16948) hydrogen bonds : bond 0.04836 ( 525) hydrogen bonds : angle 4.87873 ( 1448) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8285 (t70) cc_final: 0.8021 (t70) REVERT: A 332 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7300 (tm-30) REVERT: A 353 GLN cc_start: 0.6825 (mp10) cc_final: 0.6546 (mp10) REVERT: A 426 GLU cc_start: 0.8008 (tp30) cc_final: 0.7510 (tm-30) REVERT: A 650 LYS cc_start: 0.7940 (ptpp) cc_final: 0.7544 (ptpp) REVERT: A 653 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8714 (mt) REVERT: B 1 MET cc_start: 0.8376 (tmm) cc_final: 0.8165 (tmm) REVERT: B 95 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6689 (mm-30) REVERT: B 98 GLU cc_start: 0.7202 (tp30) cc_final: 0.6835 (tp30) REVERT: B 222 ARG cc_start: 0.7797 (ttm170) cc_final: 0.7511 (mtp85) REVERT: B 382 MET cc_start: 0.7363 (mtp) cc_final: 0.7042 (ttm) REVERT: B 560 TYR cc_start: 0.7145 (m-80) cc_final: 0.6691 (m-80) REVERT: B 587 LYS cc_start: 0.7449 (mttt) cc_final: 0.7003 (mttt) REVERT: C 18 LYS cc_start: 0.7914 (mttt) cc_final: 0.7038 (tppt) REVERT: C 38 TRP cc_start: 0.7245 (OUTLIER) cc_final: 0.6412 (m100) REVERT: C 51 MET cc_start: 0.7818 (tpp) cc_final: 0.7064 (tpp) REVERT: C 65 ARG cc_start: 0.7596 (ttt90) cc_final: 0.7198 (ttm-80) REVERT: C 171 MET cc_start: 0.8089 (mmm) cc_final: 0.7411 (mtm) REVERT: C 213 MET cc_start: 0.5513 (ptm) cc_final: 0.5099 (ptm) outliers start: 43 outliers final: 34 residues processed: 275 average time/residue: 0.1019 time to fit residues: 40.6715 Evaluate side-chains 274 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 749 GLN Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 80 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 303 ASN C 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.172019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143393 restraints weight = 18259.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146275 restraints weight = 11114.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148115 restraints weight = 7946.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149121 restraints weight = 6400.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150087 restraints weight = 5595.089| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12534 Z= 0.122 Angle : 0.630 17.768 16948 Z= 0.313 Chirality : 0.042 0.162 1855 Planarity : 0.004 0.058 2068 Dihedral : 11.229 73.584 1926 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 3.27 % Allowed : 19.33 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.22), residues: 1441 helix: 0.38 (0.20), residues: 683 sheet: -0.49 (0.54), residues: 108 loop : -2.45 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 131 TYR 0.014 0.001 TYR B 38 PHE 0.014 0.001 PHE B 108 TRP 0.014 0.001 TRP C 132 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00280 (12534) covalent geometry : angle 0.63039 (16948) hydrogen bonds : bond 0.04211 ( 525) hydrogen bonds : angle 4.64822 ( 1448) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8252 (t70) cc_final: 0.7924 (t70) REVERT: A 275 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8454 (pttt) REVERT: A 353 GLN cc_start: 0.6865 (mp10) cc_final: 0.6587 (mp10) REVERT: A 356 LYS cc_start: 0.7691 (mptt) cc_final: 0.7381 (mmtm) REVERT: A 426 GLU cc_start: 0.8005 (tp30) cc_final: 0.7500 (tm-30) REVERT: A 475 GLU cc_start: 0.7631 (mp0) cc_final: 0.7345 (pm20) REVERT: A 497 MET cc_start: 0.7107 (mmm) cc_final: 0.6732 (mmp) REVERT: B 1 MET cc_start: 0.8351 (tmm) cc_final: 0.8091 (tmm) REVERT: B 14 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8398 (tp) REVERT: B 95 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6796 (mm-30) REVERT: B 98 GLU cc_start: 0.7085 (tp30) cc_final: 0.6752 (tp30) REVERT: B 222 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7420 (mmm-85) REVERT: B 560 TYR cc_start: 0.7099 (m-80) cc_final: 0.6679 (m-80) REVERT: B 587 LYS cc_start: 0.7303 (mttt) cc_final: 0.6865 (mttt) REVERT: B 599 MET cc_start: 0.8113 (tpp) cc_final: 0.7826 (tpp) REVERT: B 751 LEU cc_start: 0.8658 (tp) cc_final: 0.8212 (pp) REVERT: C 18 LYS cc_start: 0.7884 (mttt) cc_final: 0.7044 (tppt) REVERT: C 38 TRP cc_start: 0.7104 (OUTLIER) cc_final: 0.6366 (m100) REVERT: C 51 MET cc_start: 0.7852 (tpp) cc_final: 0.7127 (tpp) REVERT: C 65 ARG cc_start: 0.7724 (ttt90) cc_final: 0.7308 (ttm-80) REVERT: C 171 MET cc_start: 0.8048 (mmm) cc_final: 0.7378 (mtm) REVERT: C 213 MET cc_start: 0.5294 (ptm) cc_final: 0.4900 (ptm) outliers start: 42 outliers final: 28 residues processed: 285 average time/residue: 0.1072 time to fit residues: 44.4185 Evaluate side-chains 277 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 137 optimal weight: 8.9990 chunk 124 optimal weight: 0.0370 chunk 122 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 120 optimal weight: 3.9990 overall best weight: 1.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.168447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139452 restraints weight = 18643.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142223 restraints weight = 11498.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144031 restraints weight = 8311.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145238 restraints weight = 6750.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145878 restraints weight = 5879.159| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12534 Z= 0.187 Angle : 0.697 17.475 16948 Z= 0.350 Chirality : 0.044 0.189 1855 Planarity : 0.004 0.053 2068 Dihedral : 11.322 73.474 1926 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 2.81 % Allowed : 19.88 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.22), residues: 1441 helix: 0.36 (0.20), residues: 677 sheet: -0.60 (0.53), residues: 108 loop : -2.42 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 131 TYR 0.015 0.002 TYR B 38 PHE 0.021 0.002 PHE C 212 TRP 0.016 0.002 TRP B 386 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00436 (12534) covalent geometry : angle 0.69684 (16948) hydrogen bonds : bond 0.04875 ( 525) hydrogen bonds : angle 4.85957 ( 1448) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8281 (t70) cc_final: 0.7858 (t70) REVERT: A 332 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 353 GLN cc_start: 0.6933 (mp10) cc_final: 0.6637 (mp10) REVERT: A 426 GLU cc_start: 0.7996 (tp30) cc_final: 0.7502 (tm-30) REVERT: A 497 MET cc_start: 0.7171 (mmm) cc_final: 0.6726 (mmp) REVERT: B 1 MET cc_start: 0.8280 (tmm) cc_final: 0.8079 (tmm) REVERT: B 2 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6961 (mm-30) REVERT: B 95 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6642 (mm-30) REVERT: B 98 GLU cc_start: 0.7135 (tp30) cc_final: 0.6837 (tp30) REVERT: B 560 TYR cc_start: 0.7217 (m-80) cc_final: 0.6726 (m-80) REVERT: B 587 LYS cc_start: 0.7347 (mttt) cc_final: 0.6921 (mttt) REVERT: B 751 LEU cc_start: 0.8615 (tp) cc_final: 0.8133 (pp) REVERT: C 18 LYS cc_start: 0.7934 (mttt) cc_final: 0.7053 (tppt) REVERT: C 38 TRP cc_start: 0.7145 (OUTLIER) cc_final: 0.6263 (m100) REVERT: C 41 SER cc_start: 0.7168 (p) cc_final: 0.6961 (m) REVERT: C 51 MET cc_start: 0.7741 (tpp) cc_final: 0.6853 (tpp) REVERT: C 55 MET cc_start: 0.4365 (mmp) cc_final: 0.3827 (mmm) REVERT: C 65 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7647 (ttm-80) REVERT: C 171 MET cc_start: 0.8092 (mmm) cc_final: 0.7336 (mtm) REVERT: C 213 MET cc_start: 0.5543 (ptm) cc_final: 0.5145 (ptm) REVERT: C 232 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7685 (mtm-85) outliers start: 36 outliers final: 31 residues processed: 269 average time/residue: 0.1006 time to fit residues: 40.1067 Evaluate side-chains 274 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 26 GLN C 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143635 restraints weight = 18526.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146519 restraints weight = 11389.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148201 restraints weight = 8137.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149583 restraints weight = 6592.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150296 restraints weight = 5708.831| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12534 Z= 0.125 Angle : 0.654 17.809 16948 Z= 0.324 Chirality : 0.042 0.174 1855 Planarity : 0.004 0.058 2068 Dihedral : 11.196 73.541 1926 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 2.65 % Allowed : 20.34 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1441 helix: 0.54 (0.20), residues: 683 sheet: -0.44 (0.54), residues: 108 loop : -2.40 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 131 TYR 0.012 0.001 TYR B 38 PHE 0.014 0.001 PHE B 108 TRP 0.014 0.001 TRP C 132 HIS 0.003 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00292 (12534) covalent geometry : angle 0.65374 (16948) hydrogen bonds : bond 0.04100 ( 525) hydrogen bonds : angle 4.61749 ( 1448) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8185 (t70) cc_final: 0.7901 (t70) REVERT: A 275 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8431 (pttt) REVERT: A 297 MET cc_start: 0.6766 (mmt) cc_final: 0.6111 (mmt) REVERT: A 353 GLN cc_start: 0.6946 (mp10) cc_final: 0.6708 (mp10) REVERT: A 356 LYS cc_start: 0.7751 (mptt) cc_final: 0.7473 (mmtm) REVERT: A 408 GLU cc_start: 0.7610 (pm20) cc_final: 0.7324 (pm20) REVERT: A 426 GLU cc_start: 0.8039 (tp30) cc_final: 0.7376 (tm-30) REVERT: A 497 MET cc_start: 0.7150 (mmm) cc_final: 0.6667 (mmp) REVERT: A 601 ARG cc_start: 0.8399 (mmt180) cc_final: 0.8083 (mmm160) REVERT: B 2 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6822 (mm-30) REVERT: B 14 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8436 (tp) REVERT: B 95 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6769 (mm-30) REVERT: B 182 LYS cc_start: 0.7010 (mttp) cc_final: 0.6652 (mtmm) REVERT: B 218 GLU cc_start: 0.8314 (tp30) cc_final: 0.8104 (tm-30) REVERT: B 222 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7677 (mtm180) REVERT: B 334 LEU cc_start: 0.8952 (tp) cc_final: 0.8623 (tp) REVERT: B 374 LYS cc_start: 0.7562 (mmtt) cc_final: 0.7211 (mmtp) REVERT: B 560 TYR cc_start: 0.7104 (m-80) cc_final: 0.6693 (m-80) REVERT: B 751 LEU cc_start: 0.8669 (tp) cc_final: 0.8223 (pp) REVERT: C 13 ASN cc_start: 0.8411 (t0) cc_final: 0.7699 (m-40) REVERT: C 18 LYS cc_start: 0.7890 (mttt) cc_final: 0.7046 (tppt) REVERT: C 38 TRP cc_start: 0.7119 (OUTLIER) cc_final: 0.6298 (m100) REVERT: C 51 MET cc_start: 0.7903 (tpp) cc_final: 0.7030 (tpp) REVERT: C 55 MET cc_start: 0.4039 (mmp) cc_final: 0.3486 (mmm) REVERT: C 65 ARG cc_start: 0.7899 (ttt90) cc_final: 0.7656 (ttm-80) REVERT: C 171 MET cc_start: 0.8044 (mmm) cc_final: 0.7399 (mtm) REVERT: C 213 MET cc_start: 0.5345 (ptm) cc_final: 0.4933 (ptm) REVERT: C 232 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7628 (mtm-85) outliers start: 34 outliers final: 24 residues processed: 289 average time/residue: 0.1112 time to fit residues: 46.4449 Evaluate side-chains 277 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143177 restraints weight = 18497.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145966 restraints weight = 11356.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147788 restraints weight = 8180.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149053 restraints weight = 6602.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149640 restraints weight = 5729.090| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 12534 Z= 0.212 Angle : 0.886 59.198 16948 Z= 0.489 Chirality : 0.044 0.545 1855 Planarity : 0.004 0.061 2068 Dihedral : 11.212 73.550 1926 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.11 % Favored : 93.82 % Rotamer: Outliers : 2.57 % Allowed : 21.28 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.22), residues: 1441 helix: 0.53 (0.20), residues: 685 sheet: -0.58 (0.53), residues: 108 loop : -2.40 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.050 0.002 TYR B 320 PHE 0.013 0.001 PHE A 645 TRP 0.013 0.001 TRP C 132 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00457 (12534) covalent geometry : angle 0.88589 (16948) hydrogen bonds : bond 0.04280 ( 525) hydrogen bonds : angle 4.66760 ( 1448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.53 seconds wall clock time: 35 minutes 22.91 seconds (2122.91 seconds total)