Starting phenix.real_space_refine on Wed Jul 30 14:28:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kuk_9578/07_2025/6kuk_9578_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kuk_9578/07_2025/6kuk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kuk_9578/07_2025/6kuk_9578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kuk_9578/07_2025/6kuk_9578.map" model { file = "/net/cci-nas-00/data/ceres_data/6kuk_9578/07_2025/6kuk_9578_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kuk_9578/07_2025/6kuk_9578_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 2, '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: 8.00, per 1000 atoms: 0.65 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: 2.90 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 3.44 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: 3.59 Time building geometry restraints manager: 3.44 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: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.160 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.970 ------------------------------------------------------------------------------- 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 : 6.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.044 0.004 TRP A 386 HIS 0.012 0.003 HIS A 451 PHE 0.033 0.004 PHE B 122 TYR 0.033 0.003 TYR B 38 ARG 0.009 0.001 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.16545 ( 525) hydrogen bonds : angle 9.11073 ( 1448) covalent geometry : bond 0.00790 (12534) covalent geometry : angle 1.02507 (16948) *********************** 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 : 1.383 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: 0.8426 (tmmt) cc_final: 0.7937 (tmmt) REVERT: A 277 HIS cc_start: 0.6382 (t70) cc_final: 0.6097 (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: 0.6774 (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: 0.7697 (pttp) REVERT: B 47 TYR cc_start: 0.8098 (m-10) cc_final: 0.7856 (m-10) REVERT: B 140 MET cc_start: 0.7415 (mtt) cc_final: 0.7012 (mtt) REVERT: B 147 GLN cc_start: 0.8495 (tp-100) cc_final: 0.7534 (tm-30) REVERT: B 182 LYS cc_start: 0.7447 (mtmt) cc_final: 0.6930 (mtmm) REVERT: B 410 MET cc_start: 0.5452 (mtp) cc_final: 0.5174 (mtp) 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: 0.6548 (t) REVERT: B 560 TYR cc_start: 0.7239 (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: 0.7535 (m-10) cc_final: 0.6901 (m-80) REVERT: C 18 LYS cc_start: 0.7199 (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: 0.2974 time to fit residues: 182.7349 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 : 1.381 ------------------------------------------------------------------------------- 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 123 optimal weight: 2.9990 chunk 110 optimal weight: 0.0070 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 477 ASN C 148 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147456 restraints weight = 18007.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150399 restraints weight = 11070.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152281 restraints weight = 7982.283| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12534 Z= 0.135 Angle : 0.661 16.852 16948 Z= 0.338 Chirality : 0.043 0.178 1855 Planarity : 0.005 0.055 2068 Dihedral : 11.733 73.843 1930 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 2.88 % Allowed : 9.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.19), residues: 1441 helix: -1.28 (0.18), residues: 659 sheet: -1.36 (0.52), residues: 109 loop : -2.96 (0.20), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 386 HIS 0.004 0.001 HIS A 490 PHE 0.028 0.001 PHE B 108 TYR 0.014 0.001 TYR B 692 ARG 0.005 0.001 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 525) hydrogen bonds : angle 5.43872 ( 1448) covalent geometry : bond 0.00288 (12534) covalent geometry : angle 0.66051 (16948) *********************** 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 379 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 342 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8039 (pt) REVERT: A 231 ASP cc_start: 0.8690 (t70) cc_final: 0.8268 (t70) REVERT: A 277 HIS cc_start: 0.6446 (t70) cc_final: 0.6215 (t-90) REVERT: A 290 ASP cc_start: 0.7500 (m-30) cc_final: 0.7292 (m-30) REVERT: A 318 LEU cc_start: 0.8851 (tp) cc_final: 0.8605 (tp) REVERT: A 367 GLN cc_start: 0.6966 (pt0) cc_final: 0.6733 (mt0) REVERT: A 416 MET cc_start: 0.8677 (ppp) cc_final: 0.7961 (ppp) REVERT: A 442 LYS cc_start: 0.8983 (tttt) cc_final: 0.8653 (tttm) REVERT: A 653 LEU cc_start: 0.8774 (mm) cc_final: 0.8512 (mp) REVERT: B 133 ASP cc_start: 0.8308 (t0) cc_final: 0.8100 (t0) REVERT: B 147 GLN cc_start: 0.8682 (tp40) cc_final: 0.7573 (tm-30) REVERT: B 182 LYS cc_start: 0.7316 (mtmt) cc_final: 0.6954 (mtmm) REVERT: B 259 THR cc_start: 0.8366 (p) cc_final: 0.8108 (t) REVERT: B 262 GLN cc_start: 0.8397 (tt0) cc_final: 0.7995 (tm-30) REVERT: B 423 MET cc_start: 0.8539 (mtm) cc_final: 0.8304 (mtp) REVERT: B 515 THR cc_start: 0.6689 (p) cc_final: 0.6376 (t) REVERT: B 560 TYR cc_start: 0.7308 (m-80) cc_final: 0.6907 (m-80) REVERT: B 587 LYS cc_start: 0.7382 (mttt) cc_final: 0.7081 (mttt) REVERT: B 685 TYR cc_start: 0.7696 (m-10) cc_final: 0.7352 (m-80) REVERT: C 18 LYS cc_start: 0.7295 (mttt) cc_final: 0.6705 (tppt) REVERT: C 51 MET cc_start: 0.7364 (tpp) cc_final: 0.6491 (tpp) REVERT: C 125 LYS cc_start: 0.8461 (mttt) cc_final: 0.8237 (mtmt) REVERT: C 129 LYS cc_start: 0.7172 (tmtt) cc_final: 0.6663 (tptt) REVERT: C 213 MET cc_start: 0.5432 (ptm) cc_final: 0.5014 (ptm) REVERT: C 228 PHE cc_start: 0.7792 (p90) cc_final: 0.7555 (p90) outliers start: 37 outliers final: 23 residues processed: 361 average time/residue: 0.3544 time to fit residues: 182.0968 Evaluate side-chains 305 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 124 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 312 ASN C 141 ASN C 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.175006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145902 restraints weight = 18340.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148922 restraints weight = 11178.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.150899 restraints weight = 7982.580| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12534 Z= 0.130 Angle : 0.625 16.224 16948 Z= 0.314 Chirality : 0.042 0.157 1855 Planarity : 0.004 0.053 2068 Dihedral : 11.438 73.842 1926 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 3.04 % Allowed : 12.70 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.21), residues: 1441 helix: -0.42 (0.19), residues: 675 sheet: -1.25 (0.49), residues: 127 loop : -2.65 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 386 HIS 0.004 0.001 HIS A 316 PHE 0.022 0.001 PHE B 108 TYR 0.027 0.001 TYR B 320 ARG 0.004 0.001 ARG B 241 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 525) hydrogen bonds : angle 4.84336 ( 1448) covalent geometry : bond 0.00286 (12534) covalent geometry : angle 0.62488 (16948) *********************** 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 339 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 300 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8642 (t70) cc_final: 0.8129 (t70) REVERT: A 235 ARG cc_start: 0.8487 (tpp-160) cc_final: 0.8262 (tpp-160) REVERT: A 353 GLN cc_start: 0.7067 (mp10) cc_final: 0.6696 (mp10) REVERT: A 367 GLN cc_start: 0.7018 (pt0) cc_final: 0.6770 (mt0) REVERT: A 416 MET cc_start: 0.8481 (ppp) cc_final: 0.8109 (ppp) REVERT: A 653 LEU cc_start: 0.8788 (mm) cc_final: 0.8535 (mp) REVERT: B 147 GLN cc_start: 0.8728 (tp40) cc_final: 0.7648 (tm-30) REVERT: B 182 LYS cc_start: 0.7196 (mtmt) cc_final: 0.6777 (mtmm) REVERT: B 262 GLN cc_start: 0.8388 (tt0) cc_final: 0.8107 (tt0) REVERT: B 515 THR cc_start: 0.6615 (p) cc_final: 0.6270 (t) REVERT: B 560 TYR cc_start: 0.7304 (m-80) cc_final: 0.6835 (m-80) REVERT: B 587 LYS cc_start: 0.7522 (mttt) cc_final: 0.7241 (mttt) REVERT: B 685 TYR cc_start: 0.7765 (m-10) cc_final: 0.7516 (m-80) REVERT: C 18 LYS cc_start: 0.7284 (mttt) cc_final: 0.6687 (tppt) REVERT: C 51 MET cc_start: 0.7347 (tpp) cc_final: 0.6425 (tpp) REVERT: C 55 MET cc_start: 0.4317 (mmp) cc_final: 0.3852 (mmm) REVERT: C 171 MET cc_start: 0.8041 (mmm) cc_final: 0.7166 (mtm) REVERT: C 213 MET cc_start: 0.5468 (ptm) cc_final: 0.5014 (ptm) outliers start: 39 outliers final: 25 residues processed: 320 average time/residue: 0.2499 time to fit residues: 114.7587 Evaluate side-chains 286 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 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 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 151 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 ASP 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 705 ILE Chi-restraints excluded: chain C residue 3 LEU 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 4 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 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 = 0.4001 r_free = 0.4001 target = 0.174755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145477 restraints weight = 18177.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148464 restraints weight = 11216.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150449 restraints weight = 8027.361| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12534 Z= 0.137 Angle : 0.631 16.691 16948 Z= 0.317 Chirality : 0.042 0.168 1855 Planarity : 0.004 0.045 2068 Dihedral : 11.348 73.727 1926 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 2.73 % Allowed : 14.96 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.21), residues: 1441 helix: -0.05 (0.20), residues: 676 sheet: -1.11 (0.51), residues: 119 loop : -2.55 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 247 HIS 0.004 0.001 HIS A 451 PHE 0.036 0.001 PHE B 108 TYR 0.011 0.001 TYR B 560 ARG 0.002 0.000 ARG A 568 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 525) hydrogen bonds : angle 4.74267 ( 1448) covalent geometry : bond 0.00308 (12534) covalent geometry : angle 0.63079 (16948) *********************** 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 317 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8569 (t70) cc_final: 0.7911 (t70) REVERT: A 353 GLN cc_start: 0.7098 (mp10) cc_final: 0.6746 (mp10) REVERT: A 367 GLN cc_start: 0.7046 (pt0) cc_final: 0.6713 (mt0) REVERT: A 650 LYS cc_start: 0.8005 (ptpp) cc_final: 0.7485 (ptpp) REVERT: A 653 LEU cc_start: 0.8854 (mm) cc_final: 0.8638 (mp) REVERT: A 656 LEU cc_start: 0.8927 (tt) cc_final: 0.8392 (tp) REVERT: B 1 MET cc_start: 0.8070 (tmm) cc_final: 0.7853 (tmm) REVERT: B 95 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6502 (mm-30) REVERT: B 98 GLU cc_start: 0.7099 (tp30) cc_final: 0.6587 (tm-30) REVERT: B 147 GLN cc_start: 0.8719 (tp40) cc_final: 0.7673 (tm-30) REVERT: B 182 LYS cc_start: 0.6929 (mtmt) cc_final: 0.6552 (mtmm) REVERT: B 222 ARG cc_start: 0.7784 (ttm170) cc_final: 0.7549 (mmm-85) REVERT: B 461 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6743 (tt0) REVERT: B 515 THR cc_start: 0.6647 (p) cc_final: 0.6325 (t) REVERT: B 560 TYR cc_start: 0.7257 (m-80) cc_final: 0.6783 (m-80) REVERT: B 587 LYS cc_start: 0.7608 (mttt) cc_final: 0.7314 (mttt) REVERT: C 18 LYS cc_start: 0.7663 (mttt) cc_final: 0.6988 (tppt) REVERT: C 51 MET cc_start: 0.7406 (tpp) cc_final: 0.6386 (tpp) REVERT: C 55 MET cc_start: 0.4369 (mmp) cc_final: 0.3967 (mmm) REVERT: C 65 ARG cc_start: 0.7419 (ttt90) cc_final: 0.7064 (ttm-80) REVERT: C 171 MET cc_start: 0.8012 (mmm) cc_final: 0.7285 (mtm) REVERT: C 213 MET cc_start: 0.5445 (ptm) cc_final: 0.5007 (ptm) outliers start: 35 outliers final: 28 residues processed: 303 average time/residue: 0.2642 time to fit residues: 113.3234 Evaluate side-chains 290 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 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 B residue 63 ILE 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 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 B residue 743 ILE Chi-restraints excluded: chain C residue 3 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.170890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141386 restraints weight = 18398.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144191 restraints weight = 11490.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146087 restraints weight = 8343.779| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 12534 Z= 0.184 Angle : 0.672 16.775 16948 Z= 0.339 Chirality : 0.044 0.153 1855 Planarity : 0.004 0.045 2068 Dihedral : 11.375 73.547 1926 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 3.51 % Allowed : 16.06 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.21), residues: 1441 helix: -0.01 (0.19), residues: 676 sheet: -1.23 (0.51), residues: 119 loop : -2.51 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 386 HIS 0.006 0.001 HIS A 451 PHE 0.030 0.002 PHE B 108 TYR 0.009 0.002 TYR B 685 ARG 0.011 0.001 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 525) hydrogen bonds : angle 4.90768 ( 1448) covalent geometry : bond 0.00425 (12534) covalent geometry : angle 0.67230 (16948) *********************** 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 304 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8407 (t70) cc_final: 0.8027 (t70) REVERT: A 367 GLN cc_start: 0.7030 (pt0) cc_final: 0.6712 (mt0) REVERT: B 55 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7340 (pm20) REVERT: B 95 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6457 (mm-30) REVERT: B 147 GLN cc_start: 0.8757 (tp40) cc_final: 0.7658 (tm-30) REVERT: B 222 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7532 (mmm-85) REVERT: B 515 THR cc_start: 0.6936 (p) cc_final: 0.6619 (t) REVERT: B 560 TYR cc_start: 0.7384 (m-80) cc_final: 0.6839 (m-80) REVERT: B 587 LYS cc_start: 0.7699 (mttt) cc_final: 0.7450 (mttt) REVERT: C 18 LYS cc_start: 0.7668 (mttt) cc_final: 0.6998 (tppt) REVERT: C 51 MET cc_start: 0.7417 (tpp) cc_final: 0.6366 (tpp) REVERT: C 55 MET cc_start: 0.4734 (mmp) cc_final: 0.4361 (mmm) REVERT: C 65 ARG cc_start: 0.7636 (ttt90) cc_final: 0.7223 (ttm-80) REVERT: C 147 LYS cc_start: 0.6939 (tppt) cc_final: 0.6570 (tppp) REVERT: C 171 MET cc_start: 0.8176 (mmm) cc_final: 0.7457 (mtm) REVERT: C 213 MET cc_start: 0.5460 (ptm) cc_final: 0.5038 (ptm) REVERT: C 232 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7762 (mtm-85) outliers start: 45 outliers final: 32 residues processed: 285 average time/residue: 0.2450 time to fit residues: 99.9331 Evaluate side-chains 275 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 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 151 ASP 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 135 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 126 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.173973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144442 restraints weight = 18556.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147354 restraints weight = 11410.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149314 restraints weight = 8204.175| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12534 Z= 0.125 Angle : 0.617 17.346 16948 Z= 0.310 Chirality : 0.041 0.154 1855 Planarity : 0.004 0.043 2068 Dihedral : 11.272 73.659 1926 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 3.20 % Allowed : 16.76 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.22), residues: 1441 helix: 0.20 (0.20), residues: 683 sheet: -1.05 (0.52), residues: 117 loop : -2.43 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 386 HIS 0.003 0.001 HIS A 451 PHE 0.021 0.001 PHE B 108 TYR 0.011 0.001 TYR B 685 ARG 0.007 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 525) hydrogen bonds : angle 4.72759 ( 1448) covalent geometry : bond 0.00284 (12534) covalent geometry : angle 0.61743 (16948) *********************** 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 312 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8303 (t70) cc_final: 0.7795 (t70) REVERT: A 353 GLN cc_start: 0.7274 (mp10) cc_final: 0.7072 (mp10) REVERT: A 367 GLN cc_start: 0.7003 (pt0) cc_final: 0.6695 (mt0) REVERT: A 497 MET cc_start: 0.7117 (mmm) cc_final: 0.6737 (mmp) REVERT: A 601 ARG cc_start: 0.8369 (mmt180) cc_final: 0.8076 (mtp85) REVERT: A 650 LYS cc_start: 0.8019 (ptpp) cc_final: 0.7564 (ptpp) REVERT: B 14 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8337 (tp) REVERT: B 47 TYR cc_start: 0.7777 (m-10) cc_final: 0.7171 (m-10) REVERT: B 55 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7253 (pm20) REVERT: B 95 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6657 (mm-30) REVERT: B 182 LYS cc_start: 0.6631 (mttp) cc_final: 0.6241 (mtmm) REVERT: B 222 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7507 (mmm-85) REVERT: B 515 THR cc_start: 0.6859 (p) cc_final: 0.6561 (t) REVERT: B 560 TYR cc_start: 0.7250 (m-80) cc_final: 0.6832 (m-80) REVERT: B 587 LYS cc_start: 0.7634 (mttt) cc_final: 0.7380 (mttt) REVERT: C 18 LYS cc_start: 0.7658 (mttt) cc_final: 0.6981 (tppt) REVERT: C 38 TRP cc_start: 0.7134 (OUTLIER) cc_final: 0.6437 (m100) REVERT: C 51 MET cc_start: 0.7763 (tpp) cc_final: 0.7037 (tpp) REVERT: C 55 MET cc_start: 0.4497 (mmp) cc_final: 0.4230 (mmm) REVERT: C 65 ARG cc_start: 0.7615 (ttt90) cc_final: 0.7221 (ttm-80) REVERT: C 171 MET cc_start: 0.8134 (mmm) cc_final: 0.7423 (mtm) REVERT: C 213 MET cc_start: 0.5437 (ptm) cc_final: 0.5020 (ptm) outliers start: 41 outliers final: 29 residues processed: 295 average time/residue: 0.2485 time to fit residues: 104.2567 Evaluate side-chains 281 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 558 LEU 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 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 15 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 135 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 104 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.174715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145372 restraints weight = 18416.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148271 restraints weight = 11369.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150201 restraints weight = 8233.212| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12534 Z= 0.121 Angle : 0.602 17.337 16948 Z= 0.302 Chirality : 0.041 0.156 1855 Planarity : 0.004 0.046 2068 Dihedral : 11.206 73.680 1926 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 3.04 % Allowed : 17.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1441 helix: 0.41 (0.20), residues: 686 sheet: -0.88 (0.53), residues: 115 loop : -2.36 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 247 HIS 0.003 0.001 HIS A 451 PHE 0.020 0.001 PHE C 212 TYR 0.013 0.001 TYR B 38 ARG 0.009 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 525) hydrogen bonds : angle 4.64053 ( 1448) covalent geometry : bond 0.00278 (12534) covalent geometry : angle 0.60245 (16948) *********************** 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 303 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 GLN cc_start: 0.6916 (pt0) cc_final: 0.6673 (mt0) REVERT: A 455 ARG cc_start: 0.7519 (tpt170) cc_final: 0.7184 (tpm170) REVERT: A 582 LEU cc_start: 0.8622 (mt) cc_final: 0.8420 (mt) REVERT: A 601 ARG cc_start: 0.8352 (mmt180) cc_final: 0.8079 (mtp85) REVERT: B 14 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8374 (tp) REVERT: B 47 TYR cc_start: 0.7717 (m-10) cc_final: 0.7169 (m-10) REVERT: B 55 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7231 (pm20) REVERT: B 95 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6662 (mm-30) REVERT: B 98 GLU cc_start: 0.7300 (tp30) cc_final: 0.6862 (tm-30) REVERT: B 140 MET cc_start: 0.7141 (mtt) cc_final: 0.6777 (mtt) REVERT: B 165 MET cc_start: 0.7581 (mmm) cc_final: 0.7197 (mmm) REVERT: B 182 LYS cc_start: 0.6598 (mttp) cc_final: 0.6139 (mtmm) REVERT: B 222 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7499 (mmm-85) REVERT: B 301 MET cc_start: 0.8540 (tmm) cc_final: 0.8201 (tmm) REVERT: B 334 LEU cc_start: 0.8942 (tp) cc_final: 0.8603 (tp) REVERT: B 515 THR cc_start: 0.6786 (p) cc_final: 0.6516 (t) REVERT: B 560 TYR cc_start: 0.7305 (m-80) cc_final: 0.6814 (m-80) REVERT: B 587 LYS cc_start: 0.7672 (mttt) cc_final: 0.7416 (mttt) REVERT: C 18 LYS cc_start: 0.7661 (mttt) cc_final: 0.6962 (tppt) REVERT: C 38 TRP cc_start: 0.7333 (OUTLIER) cc_final: 0.6758 (m100) REVERT: C 51 MET cc_start: 0.7733 (tpp) cc_final: 0.7058 (tpp) REVERT: C 171 MET cc_start: 0.8101 (mmm) cc_final: 0.7410 (mtm) REVERT: C 213 MET cc_start: 0.5448 (ptm) cc_final: 0.5049 (ptm) outliers start: 39 outliers final: 30 residues processed: 288 average time/residue: 0.2495 time to fit residues: 102.2175 Evaluate side-chains 276 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 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 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 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 135 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 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 = 0.4002 r_free = 0.4002 target = 0.174674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145527 restraints weight = 18563.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148467 restraints weight = 11271.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150472 restraints weight = 8036.333| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12534 Z= 0.127 Angle : 0.628 17.580 16948 Z= 0.312 Chirality : 0.041 0.155 1855 Planarity : 0.004 0.046 2068 Dihedral : 11.211 73.586 1926 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 3.35 % Allowed : 17.77 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.22), residues: 1441 helix: 0.51 (0.20), residues: 686 sheet: -0.39 (0.56), residues: 103 loop : -2.36 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 357 HIS 0.003 0.001 HIS A 451 PHE 0.018 0.001 PHE B 108 TYR 0.012 0.001 TYR B 38 ARG 0.008 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 525) hydrogen bonds : angle 4.60204 ( 1448) covalent geometry : bond 0.00293 (12534) covalent geometry : angle 0.62772 (16948) *********************** 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 304 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 412 CYS cc_start: 0.8276 (p) cc_final: 0.7759 (m) REVERT: A 455 ARG cc_start: 0.7570 (tpt170) cc_final: 0.7201 (tpm170) REVERT: A 475 GLU cc_start: 0.7555 (mp0) cc_final: 0.7259 (pm20) REVERT: A 497 MET cc_start: 0.7083 (mmm) cc_final: 0.6770 (mmp) REVERT: A 582 LEU cc_start: 0.8650 (mt) cc_final: 0.8447 (mt) REVERT: A 601 ARG cc_start: 0.8322 (mmt180) cc_final: 0.8037 (mtp85) REVERT: B 9 MET cc_start: 0.7093 (mtt) cc_final: 0.6750 (ttm) REVERT: B 47 TYR cc_start: 0.7728 (m-10) cc_final: 0.7194 (m-10) REVERT: B 55 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7221 (pm20) REVERT: B 95 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6516 (mm-30) REVERT: B 98 GLU cc_start: 0.7182 (tp30) cc_final: 0.6818 (tm-30) REVERT: B 165 MET cc_start: 0.7596 (mmm) cc_final: 0.7200 (mmm) REVERT: B 222 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7333 (mmm-85) REVERT: B 301 MET cc_start: 0.8546 (tmm) cc_final: 0.8217 (tmm) REVERT: B 334 LEU cc_start: 0.8925 (tp) cc_final: 0.8581 (tp) REVERT: B 412 MET cc_start: 0.6720 (mmp) cc_final: 0.6443 (mmp) REVERT: B 515 THR cc_start: 0.6773 (p) cc_final: 0.6509 (t) REVERT: B 560 TYR cc_start: 0.7140 (m-80) cc_final: 0.6738 (m-80) REVERT: C 13 ASN cc_start: 0.8491 (t0) cc_final: 0.7825 (m-40) REVERT: C 18 LYS cc_start: 0.7691 (mttt) cc_final: 0.7018 (tppt) REVERT: C 38 TRP cc_start: 0.7269 (OUTLIER) cc_final: 0.6675 (m100) REVERT: C 51 MET cc_start: 0.7651 (tpp) cc_final: 0.7016 (tpp) REVERT: C 171 MET cc_start: 0.8091 (mmm) cc_final: 0.7400 (mtm) REVERT: C 213 MET cc_start: 0.5464 (ptm) cc_final: 0.5070 (ptm) REVERT: C 232 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7646 (mtm-85) outliers start: 43 outliers final: 35 residues processed: 287 average time/residue: 0.2430 time to fit residues: 101.0399 Evaluate side-chains 279 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 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 558 LEU 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 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 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 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 135 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 82 optimal weight: 0.0060 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.174328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145247 restraints weight = 18500.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148204 restraints weight = 11393.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149840 restraints weight = 8162.653| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12534 Z= 0.130 Angle : 0.641 17.452 16948 Z= 0.319 Chirality : 0.041 0.159 1855 Planarity : 0.004 0.045 2068 Dihedral : 11.207 73.576 1926 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 2.73 % Allowed : 18.55 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1441 helix: 0.54 (0.20), residues: 685 sheet: -0.40 (0.56), residues: 103 loop : -2.33 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 388 HIS 0.003 0.001 HIS A 451 PHE 0.017 0.001 PHE B 108 TYR 0.012 0.001 TYR B 38 ARG 0.009 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 525) hydrogen bonds : angle 4.58049 ( 1448) covalent geometry : bond 0.00302 (12534) covalent geometry : angle 0.64094 (16948) *********************** 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 285 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 ARG cc_start: 0.7545 (tpt170) cc_final: 0.7197 (tpm170) REVERT: A 497 MET cc_start: 0.7044 (mmm) cc_final: 0.6638 (mmp) REVERT: A 582 LEU cc_start: 0.8667 (mt) cc_final: 0.8452 (mt) REVERT: A 601 ARG cc_start: 0.8314 (mmt180) cc_final: 0.8011 (mmm160) REVERT: A 653 LEU cc_start: 0.8719 (mp) cc_final: 0.8194 (mp) REVERT: B 47 TYR cc_start: 0.7728 (m-10) cc_final: 0.7175 (m-10) REVERT: B 55 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7224 (pm20) REVERT: B 95 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6471 (mm-30) REVERT: B 98 GLU cc_start: 0.7161 (tp30) cc_final: 0.6729 (tp30) REVERT: B 140 MET cc_start: 0.7021 (mtt) cc_final: 0.6707 (mtt) REVERT: B 165 MET cc_start: 0.7570 (mmm) cc_final: 0.7185 (mmm) REVERT: B 222 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7404 (mmm-85) REVERT: B 301 MET cc_start: 0.8601 (tmm) cc_final: 0.8296 (tmm) REVERT: B 313 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7855 (mm-30) REVERT: B 334 LEU cc_start: 0.8917 (tp) cc_final: 0.8581 (tp) REVERT: B 382 MET cc_start: 0.7322 (mtp) cc_final: 0.7116 (ttt) REVERT: B 515 THR cc_start: 0.6737 (p) cc_final: 0.6506 (t) REVERT: B 560 TYR cc_start: 0.7167 (m-80) cc_final: 0.6773 (m-80) REVERT: C 13 ASN cc_start: 0.8519 (t0) cc_final: 0.7738 (m-40) REVERT: C 18 LYS cc_start: 0.7714 (mttt) cc_final: 0.7019 (tppt) REVERT: C 38 TRP cc_start: 0.7277 (OUTLIER) cc_final: 0.6691 (m100) REVERT: C 51 MET cc_start: 0.7851 (tpp) cc_final: 0.7018 (tpp) REVERT: C 55 MET cc_start: 0.4105 (mmp) cc_final: 0.3574 (mmm) REVERT: C 171 MET cc_start: 0.8077 (mmm) cc_final: 0.7382 (mtm) REVERT: C 213 MET cc_start: 0.5489 (ptm) cc_final: 0.5093 (ptm) REVERT: C 232 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7689 (mtm-85) outliers start: 35 outliers final: 32 residues processed: 273 average time/residue: 0.2315 time to fit residues: 91.9889 Evaluate side-chains 277 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 558 LEU 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 181 VAL 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 C residue 3 LEU 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 135 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 116 optimal weight: 2.9990 chunk 14 optimal weight: 0.0050 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.173717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144169 restraints weight = 18524.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147082 restraints weight = 11545.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149021 restraints weight = 8331.959| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 12534 Z= 0.239 Angle : 0.883 59.199 16948 Z= 0.490 Chirality : 0.044 0.451 1855 Planarity : 0.004 0.079 2068 Dihedral : 11.239 73.576 1926 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 2.73 % Allowed : 18.94 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1441 helix: 0.52 (0.20), residues: 685 sheet: -0.55 (0.55), residues: 103 loop : -2.33 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.003 TRP A 388 HIS 0.003 0.001 HIS A 451 PHE 0.017 0.001 PHE B 108 TYR 0.068 0.002 TYR B 320 ARG 0.009 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 525) hydrogen bonds : angle 4.62570 ( 1448) covalent geometry : bond 0.00527 (12534) covalent geometry : angle 0.88337 (16948) ********************** 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 277 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 455 ARG cc_start: 0.7554 (tpt170) cc_final: 0.7195 (tpm170) REVERT: A 497 MET cc_start: 0.7050 (mmm) cc_final: 0.6642 (mmp) REVERT: A 574 MET cc_start: 0.7255 (tmt) cc_final: 0.7040 (tmt) REVERT: A 582 LEU cc_start: 0.8661 (mt) cc_final: 0.8457 (mt) REVERT: A 601 ARG cc_start: 0.8313 (mmt180) cc_final: 0.8013 (mmm160) REVERT: A 653 LEU cc_start: 0.8640 (mp) cc_final: 0.8182 (mp) REVERT: B 47 TYR cc_start: 0.7730 (m-10) cc_final: 0.7267 (m-10) REVERT: B 55 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7232 (pm20) REVERT: B 95 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6480 (mm-30) REVERT: B 98 GLU cc_start: 0.7156 (tp30) cc_final: 0.6716 (tp30) REVERT: B 140 MET cc_start: 0.7031 (mtt) cc_final: 0.6712 (mtt) REVERT: B 165 MET cc_start: 0.7605 (mmm) cc_final: 0.7183 (mmm) REVERT: B 222 ARG cc_start: 0.7735 (ttm170) cc_final: 0.7407 (mmm-85) REVERT: B 301 MET cc_start: 0.8511 (tmm) cc_final: 0.8284 (tmm) REVERT: B 334 LEU cc_start: 0.8914 (tp) cc_final: 0.8583 (tp) REVERT: B 382 MET cc_start: 0.7430 (mtp) cc_final: 0.7190 (ttt) REVERT: B 515 THR cc_start: 0.6768 (p) cc_final: 0.6505 (t) REVERT: B 560 TYR cc_start: 0.7166 (m-80) cc_final: 0.6783 (m-80) REVERT: C 13 ASN cc_start: 0.8528 (t0) cc_final: 0.7741 (m-40) REVERT: C 18 LYS cc_start: 0.7718 (mttt) cc_final: 0.7025 (tppt) REVERT: C 38 TRP cc_start: 0.7275 (OUTLIER) cc_final: 0.6681 (m100) REVERT: C 51 MET cc_start: 0.7869 (tpp) cc_final: 0.7033 (tpp) REVERT: C 55 MET cc_start: 0.4114 (mmp) cc_final: 0.3584 (mmm) REVERT: C 171 MET cc_start: 0.8077 (mmm) cc_final: 0.7387 (mtm) REVERT: C 213 MET cc_start: 0.5489 (ptm) cc_final: 0.5093 (ptm) REVERT: C 232 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7689 (mtm-85) outliers start: 35 outliers final: 32 residues processed: 264 average time/residue: 0.2262 time to fit residues: 86.9063 Evaluate side-chains 274 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 477 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 558 LEU 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 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 462 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 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 135 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 4 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 94 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 136 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.173718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144393 restraints weight = 18572.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147272 restraints weight = 11518.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149164 restraints weight = 8307.831| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 12534 Z= 0.239 Angle : 0.883 59.199 16948 Z= 0.490 Chirality : 0.044 0.451 1855 Planarity : 0.004 0.079 2068 Dihedral : 11.239 73.576 1926 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 2.57 % Allowed : 19.10 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1441 helix: 0.52 (0.20), residues: 685 sheet: -0.55 (0.55), residues: 103 loop : -2.33 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.003 TRP A 388 HIS 0.003 0.001 HIS A 451 PHE 0.017 0.001 PHE B 108 TYR 0.068 0.002 TYR B 320 ARG 0.009 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 525) hydrogen bonds : angle 4.62570 ( 1448) covalent geometry : bond 0.00527 (12534) covalent geometry : angle 0.88338 (16948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4276.04 seconds wall clock time: 76 minutes 14.27 seconds (4574.27 seconds total)