Starting phenix.real_space_refine on Thu Mar 13 21:32:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l1f_23109/03_2025/7l1f_23109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l1f_23109/03_2025/7l1f_23109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l1f_23109/03_2025/7l1f_23109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l1f_23109/03_2025/7l1f_23109.map" model { file = "/net/cci-nas-00/data/ceres_data/7l1f_23109/03_2025/7l1f_23109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l1f_23109/03_2025/7l1f_23109.cif" } resolution = 3.89 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 ------------------------------------------------------------------------------- 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= 0.021 sd= 0.103 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 35 5.49 5 S 58 5.16 5 C 5504 2.51 5 N 1473 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8825 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6708 Classifications: {'peptide': 832} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 803} Chain breaks: 3 Chain: "C" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 486 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "P" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna3p': 12} Chain: "P" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'F86': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Chain: "T" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 376 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 16} Time building chain proxies: 5.72, per 1000 atoms: 0.65 Number of scatterers: 8825 At special positions: 0 Unit cell: (86.9, 99, 122.1, 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 58 16.00 P 35 15.00 O 1755 8.00 N 1473 7.00 C 5504 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 844.8 milliseconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 46.3% alpha, 7.1% beta 9 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 123 through 130 removed outlier: 3.877A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.585A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 removed outlier: 4.418A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.690A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.576A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.733A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.335A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.930A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.655A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.656A pdb=" N ALA A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 424 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.666A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 4.144A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.978A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 480 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.568A pdb=" N GLN A 492 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 493' Processing helix chain 'A' and resid 505 through 509 removed outlier: 4.138A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.103A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.809A pdb=" N ASN A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.606A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.638A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 663 " --> pdb=" O CYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.538A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 removed outlier: 3.772A pdb=" N VAL A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 789 removed outlier: 3.906A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.567A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS A 842 " --> pdb=" O LEU A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 851 through 866 removed outlier: 4.190A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 895 removed outlier: 4.382A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 925 removed outlier: 4.312A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 94 removed outlier: 3.978A pdb=" N MET C 94 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 removed outlier: 4.219A pdb=" N ASN C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.608A pdb=" N THR C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 142 removed outlier: 3.758A pdb=" N TYR C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 4.047A pdb=" N ASN C 176 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 19 removed outlier: 3.977A pdb=" N LYS D 7 " --> pdb=" O MET D 3 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D 19 " --> pdb=" O SER D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 40 removed outlier: 3.756A pdb=" N TRP D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 62 removed outlier: 3.554A pdb=" N MET D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.524A pdb=" N ALA A 46 " --> pdb=" O PHE A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.296A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA4, first strand: chain 'A' and resid 332 through 335 removed outlier: 3.806A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 673 through 674 removed outlier: 7.215A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 386 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C 129 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 131 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 128 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 130 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN C 158 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU C 189 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE C 156 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 147 " --> pdb=" O TRP C 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 612 through 614 removed outlier: 3.818A pdb=" N HIS A 613 " --> pdb=" O PHE A 766 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 761 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 817 Processing sheet with id=AA9, first strand: chain 'A' and resid 820 through 822 removed outlier: 3.767A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1364 1.27 - 1.41: 2436 1.41 - 1.55: 5044 1.55 - 1.68: 162 1.68 - 1.82: 87 Bond restraints: 9093 Sorted by residual: bond pdb=" C11 F86 P 15 " pdb=" N5 F86 P 15 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.00e-02 1.00e+04 1.37e+02 bond pdb=" C11 F86 P 16 " pdb=" N5 F86 P 16 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.00e-02 1.00e+04 1.32e+02 bond pdb=" C11 F86 P 14 " pdb=" N5 F86 P 14 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.00e-02 1.00e+04 1.30e+02 bond pdb=" C11 F86 P 17 " pdb=" N5 F86 P 17 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.00e-02 1.00e+04 1.30e+02 bond pdb=" C12 F86 P 15 " pdb=" N2 F86 P 15 " ideal model delta sigma weight residual 1.293 1.358 -0.065 1.00e-02 1.00e+04 4.28e+01 ... (remaining 9088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 12063 3.23 - 6.47: 351 6.47 - 9.70: 61 9.70 - 12.93: 16 12.93 - 16.17: 6 Bond angle restraints: 12497 Sorted by residual: angle pdb=" C THR A 556 " pdb=" N VAL A 557 " pdb=" CA VAL A 557 " ideal model delta sigma weight residual 121.97 137.48 -15.51 1.80e+00 3.09e-01 7.42e+01 angle pdb=" C TRP C 182 " pdb=" N PRO C 183 " pdb=" CD PRO C 183 " ideal model delta sigma weight residual 120.60 104.96 15.64 2.20e+00 2.07e-01 5.06e+01 angle pdb=" CB LYS A 411 " pdb=" CG LYS A 411 " pdb=" CD LYS A 411 " ideal model delta sigma weight residual 111.30 127.43 -16.13 2.30e+00 1.89e-01 4.92e+01 angle pdb=" C7 F86 P 16 " pdb=" C5 F86 P 16 " pdb=" N1 F86 P 16 " ideal model delta sigma weight residual 107.20 113.84 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CA ASP A 304 " pdb=" CB ASP A 304 " pdb=" CG ASP A 304 " ideal model delta sigma weight residual 112.60 119.15 -6.55 1.00e+00 1.00e+00 4.28e+01 ... (remaining 12492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 5007 23.49 - 46.97: 311 46.97 - 70.46: 44 70.46 - 93.94: 8 93.94 - 117.43: 1 Dihedral angle restraints: 5371 sinusoidal: 2378 harmonic: 2993 Sorted by residual: dihedral pdb=" CA THR A 556 " pdb=" C THR A 556 " pdb=" N VAL A 557 " pdb=" CA VAL A 557 " ideal model delta harmonic sigma weight residual 180.00 148.03 31.97 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA LEU C 98 " pdb=" C LEU C 98 " pdb=" N ASP C 99 " pdb=" CA ASP C 99 " ideal model delta harmonic sigma weight residual -180.00 -149.78 -30.22 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA ALA A 762 " pdb=" C ALA A 762 " pdb=" N VAL A 763 " pdb=" CA VAL A 763 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 5368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1257 0.105 - 0.210: 138 0.210 - 0.315: 26 0.315 - 0.419: 3 0.419 - 0.524: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB VAL A 588 " pdb=" CA VAL A 588 " pdb=" CG1 VAL A 588 " pdb=" CG2 VAL A 588 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" CB THR A 556 " pdb=" CA THR A 556 " pdb=" OG1 THR A 556 " pdb=" CG2 THR A 556 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CB VAL A 476 " pdb=" CA VAL A 476 " pdb=" CG1 VAL A 476 " pdb=" CG2 VAL A 476 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.15e+00 ... (remaining 1423 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 157 " 0.021 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE A 157 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 157 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 157 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 157 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 157 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 157 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 237 " 0.007 2.00e-02 2.50e+03 2.84e-02 1.62e+01 pdb=" CG TYR A 237 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A 237 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 237 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR A 237 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 237 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 237 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 237 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 182 " 0.060 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO C 183 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " 0.034 5.00e-02 4.00e+02 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2804 2.84 - 3.35: 7268 3.35 - 3.87: 14457 3.87 - 4.38: 15613 4.38 - 4.90: 25841 Nonbonded interactions: 65983 Sorted by model distance: nonbonded pdb=" OG1 THR A 540 " pdb=" OE2 GLU A 665 " model vdw 2.323 3.040 nonbonded pdb=" OG1 THR A 246 " pdb=" O PRO A 461 " model vdw 2.330 3.040 nonbonded pdb=" O THR C 89 " pdb=" OG1 THR C 93 " model vdw 2.344 3.040 nonbonded pdb=" OG1 THR A 206 " pdb=" OD1 ASN A 209 " model vdw 2.349 3.040 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.349 3.040 ... (remaining 65978 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=0.00 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: 0.050 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 0.117 9093 Z= 0.514 Angle : 1.362 16.168 12497 Z= 0.737 Chirality : 0.075 0.524 1426 Planarity : 0.008 0.087 1466 Dihedral : 14.821 117.425 3439 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.38 (0.20), residues: 997 helix: -3.54 (0.15), residues: 411 sheet: -2.04 (0.65), residues: 61 loop : -2.45 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 29 HIS 0.017 0.002 HIS A 309 PHE 0.069 0.004 PHE A 157 TYR 0.064 0.004 TYR A 237 ARG 0.025 0.002 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7376 (tpt) cc_final: 0.6950 (tpt) REVERT: A 143 LYS cc_start: 0.7914 (tppp) cc_final: 0.7662 (tptt) REVERT: A 149 TYR cc_start: 0.8083 (m-80) cc_final: 0.7788 (m-10) REVERT: A 150 ASN cc_start: 0.7788 (m110) cc_final: 0.7513 (m110) REVERT: A 173 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7815 (ttp80) REVERT: A 283 PHE cc_start: 0.7485 (t80) cc_final: 0.7060 (t80) REVERT: A 395 CYS cc_start: 0.7589 (m) cc_final: 0.7324 (m) REVERT: A 454 ASP cc_start: 0.7414 (t0) cc_final: 0.6994 (t0) REVERT: A 691 ASN cc_start: 0.8311 (m110) cc_final: 0.8036 (m-40) REVERT: A 698 GLN cc_start: 0.7715 (mp10) cc_final: 0.7507 (mp10) REVERT: A 703 ASN cc_start: 0.8006 (m-40) cc_final: 0.7563 (m-40) REVERT: A 707 LEU cc_start: 0.8546 (tp) cc_final: 0.8315 (tp) REVERT: A 748 TYR cc_start: 0.7782 (t80) cc_final: 0.7476 (t80) REVERT: A 815 GLN cc_start: 0.7505 (mm110) cc_final: 0.7223 (mm110) REVERT: A 855 MET cc_start: 0.6818 (mtm) cc_final: 0.6117 (mtm) REVERT: A 857 GLU cc_start: 0.7442 (pm20) cc_final: 0.7214 (pm20) REVERT: A 892 HIS cc_start: 0.7798 (t70) cc_final: 0.7535 (t70) REVERT: C 129 MET cc_start: 0.6852 (ppp) cc_final: 0.6571 (ppp) REVERT: C 157 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8211 (tm-30) REVERT: D 2 LYS cc_start: 0.6639 (pttp) cc_final: 0.6289 (pttm) REVERT: D 51 LYS cc_start: 0.7629 (mptt) cc_final: 0.7409 (tptt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2329 time to fit residues: 79.2848 Evaluate side-chains 215 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN C 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.161575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139176 restraints weight = 14897.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143377 restraints weight = 8095.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146133 restraints weight = 5109.887| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9093 Z= 0.213 Angle : 0.664 7.989 12497 Z= 0.354 Chirality : 0.044 0.306 1426 Planarity : 0.005 0.077 1466 Dihedral : 12.211 123.538 1567 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.02 % Allowed : 9.43 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -3.15 (0.22), residues: 997 helix: -1.78 (0.21), residues: 435 sheet: -2.43 (0.55), residues: 77 loop : -2.27 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 268 HIS 0.004 0.001 HIS A 381 PHE 0.033 0.002 PHE A 157 TYR 0.015 0.002 TYR A 273 ARG 0.006 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7508 (tpt) cc_final: 0.7150 (tpt) REVERT: A 150 ASN cc_start: 0.7908 (m110) cc_final: 0.7582 (m110) REVERT: A 167 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: A 242 MET cc_start: 0.7147 (mtp) cc_final: 0.6812 (mtp) REVERT: A 357 GLN cc_start: 0.6702 (mp10) cc_final: 0.6347 (mp10) REVERT: A 365 ARG cc_start: 0.7272 (mtt90) cc_final: 0.7002 (mtt90) REVERT: A 395 CYS cc_start: 0.7459 (m) cc_final: 0.7247 (m) REVERT: A 454 ASP cc_start: 0.7323 (t0) cc_final: 0.6951 (t0) REVERT: A 661 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7026 (mm-40) REVERT: A 698 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: A 703 ASN cc_start: 0.8143 (m110) cc_final: 0.7680 (m110) REVERT: A 765 CYS cc_start: 0.8537 (t) cc_final: 0.8263 (t) REVERT: A 766 PHE cc_start: 0.8653 (p90) cc_final: 0.8023 (p90) REVERT: A 782 PHE cc_start: 0.7314 (m-80) cc_final: 0.6850 (t80) REVERT: A 815 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7072 (mm110) REVERT: A 855 MET cc_start: 0.6633 (mtm) cc_final: 0.6033 (mtm) REVERT: A 889 ARG cc_start: 0.7605 (tmm160) cc_final: 0.7139 (tmm160) REVERT: A 892 HIS cc_start: 0.7829 (t70) cc_final: 0.7621 (t70) REVERT: A 919 GLU cc_start: 0.7814 (mp0) cc_final: 0.7415 (mp0) REVERT: A 924 MET cc_start: 0.7368 (tpp) cc_final: 0.7019 (tpp) REVERT: C 117 LEU cc_start: 0.8004 (tt) cc_final: 0.7786 (tt) REVERT: C 129 MET cc_start: 0.6946 (ppp) cc_final: 0.6381 (ppp) REVERT: C 157 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8085 (tm-30) REVERT: D 2 LYS cc_start: 0.6643 (pttp) cc_final: 0.6219 (pttm) outliers start: 18 outliers final: 13 residues processed: 242 average time/residue: 0.2266 time to fit residues: 74.3988 Evaluate side-chains 244 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.155249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133289 restraints weight = 15243.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137315 restraints weight = 8248.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.139962 restraints weight = 5240.423| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9093 Z= 0.438 Angle : 0.759 7.277 12497 Z= 0.412 Chirality : 0.049 0.369 1426 Planarity : 0.006 0.058 1466 Dihedral : 12.366 129.784 1567 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.82 % Allowed : 13.47 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.66 (0.23), residues: 997 helix: -1.06 (0.23), residues: 433 sheet: -2.80 (0.53), residues: 67 loop : -2.26 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 182 HIS 0.006 0.001 HIS A 872 PHE 0.031 0.003 PHE A 415 TYR 0.029 0.003 TYR A 273 ARG 0.007 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7904 (mttt) cc_final: 0.7595 (mttm) REVERT: A 124 MET cc_start: 0.7615 (tpt) cc_final: 0.7026 (tpt) REVERT: A 150 ASN cc_start: 0.8032 (m110) cc_final: 0.7693 (m110) REVERT: A 167 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: A 183 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7577 (ttp-170) REVERT: A 297 ASN cc_start: 0.7971 (p0) cc_final: 0.7769 (p0) REVERT: A 365 ARG cc_start: 0.7223 (mtt90) cc_final: 0.6972 (mtt90) REVERT: A 454 ASP cc_start: 0.7535 (t0) cc_final: 0.7264 (t0) REVERT: A 492 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6535 (mt0) REVERT: A 591 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8331 (p) REVERT: A 703 ASN cc_start: 0.8153 (m110) cc_final: 0.7739 (m110) REVERT: A 765 CYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8259 (t) REVERT: A 782 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.6996 (t80) REVERT: A 819 LEU cc_start: 0.8910 (tp) cc_final: 0.8451 (tp) REVERT: A 855 MET cc_start: 0.6732 (mtm) cc_final: 0.6051 (mtm) REVERT: A 889 ARG cc_start: 0.7752 (tmm160) cc_final: 0.7171 (tmm160) REVERT: A 917 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 919 GLU cc_start: 0.7781 (mp0) cc_final: 0.7265 (mp0) REVERT: A 924 MET cc_start: 0.7283 (tpp) cc_final: 0.6899 (ttm) REVERT: C 157 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7985 (tm-30) REVERT: D 7 LYS cc_start: 0.7814 (mttm) cc_final: 0.7560 (mttp) outliers start: 34 outliers final: 25 residues processed: 220 average time/residue: 0.2480 time to fit residues: 74.9029 Evaluate side-chains 237 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.137327 restraints weight = 15165.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141494 restraints weight = 8281.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144207 restraints weight = 5257.537| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9093 Z= 0.177 Angle : 0.586 7.015 12497 Z= 0.314 Chirality : 0.043 0.298 1426 Planarity : 0.004 0.048 1466 Dihedral : 11.801 122.831 1567 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.37 % Allowed : 16.84 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.95 (0.25), residues: 997 helix: -0.39 (0.24), residues: 430 sheet: -2.50 (0.52), residues: 73 loop : -1.92 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 268 HIS 0.002 0.001 HIS A 295 PHE 0.027 0.001 PHE A 415 TYR 0.013 0.001 TYR A 294 ARG 0.006 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7902 (mttt) cc_final: 0.7238 (mttm) REVERT: A 124 MET cc_start: 0.7602 (tpt) cc_final: 0.7219 (tpt) REVERT: A 150 ASN cc_start: 0.7876 (m110) cc_final: 0.7536 (m110) REVERT: A 249 ARG cc_start: 0.7774 (ttm110) cc_final: 0.7409 (ttm-80) REVERT: A 297 ASN cc_start: 0.7919 (p0) cc_final: 0.7626 (p0) REVERT: A 365 ARG cc_start: 0.7223 (mtt90) cc_final: 0.6979 (mtt90) REVERT: A 380 MET cc_start: 0.7341 (tmm) cc_final: 0.7084 (tmm) REVERT: A 438 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8070 (mmtt) REVERT: A 454 ASP cc_start: 0.7470 (t0) cc_final: 0.7122 (t0) REVERT: A 513 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7970 (ttm-80) REVERT: A 703 ASN cc_start: 0.8046 (m110) cc_final: 0.7588 (m110) REVERT: A 765 CYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7994 (t) REVERT: A 782 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6902 (t80) REVERT: A 807 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8323 (pttm) REVERT: A 819 LEU cc_start: 0.8592 (tp) cc_final: 0.8344 (tp) REVERT: A 855 MET cc_start: 0.6603 (mtm) cc_final: 0.5929 (mtm) REVERT: A 881 PHE cc_start: 0.7637 (t80) cc_final: 0.7427 (t80) REVERT: A 886 GLN cc_start: 0.7777 (mm-40) cc_final: 0.6443 (mm-40) REVERT: A 889 ARG cc_start: 0.7669 (tmm160) cc_final: 0.6933 (tmm160) REVERT: A 917 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7319 (mm-30) REVERT: A 919 GLU cc_start: 0.7685 (mp0) cc_final: 0.7236 (mp0) REVERT: C 157 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8113 (tm-30) outliers start: 30 outliers final: 20 residues processed: 232 average time/residue: 0.2168 time to fit residues: 68.2778 Evaluate side-chains 240 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 3 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.156911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134818 restraints weight = 15080.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138949 restraints weight = 8242.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141612 restraints weight = 5218.750| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9093 Z= 0.291 Angle : 0.648 10.491 12497 Z= 0.342 Chirality : 0.045 0.301 1426 Planarity : 0.004 0.057 1466 Dihedral : 11.802 124.219 1567 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.49 % Allowed : 17.96 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.80 (0.25), residues: 997 helix: -0.18 (0.25), residues: 429 sheet: -3.03 (0.47), residues: 79 loop : -1.79 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 216 HIS 0.004 0.001 HIS A 133 PHE 0.028 0.002 PHE A 415 TYR 0.020 0.002 TYR A 273 ARG 0.006 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7934 (mttt) cc_final: 0.7325 (mttm) REVERT: A 86 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.5161 (mt) REVERT: A 124 MET cc_start: 0.7550 (tpt) cc_final: 0.7250 (tpt) REVERT: A 150 ASN cc_start: 0.7940 (m110) cc_final: 0.7618 (m110) REVERT: A 183 ARG cc_start: 0.7656 (ttm170) cc_final: 0.7390 (ttp-170) REVERT: A 249 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7469 (ttm-80) REVERT: A 365 ARG cc_start: 0.7256 (mtt90) cc_final: 0.6994 (mtt90) REVERT: A 380 MET cc_start: 0.7452 (tmm) cc_final: 0.7231 (tmm) REVERT: A 438 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8173 (mmtt) REVERT: A 454 ASP cc_start: 0.7475 (t0) cc_final: 0.7189 (t0) REVERT: A 703 ASN cc_start: 0.8134 (m110) cc_final: 0.7733 (m110) REVERT: A 765 CYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7954 (t) REVERT: A 782 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7016 (t80) REVERT: A 807 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8325 (pttm) REVERT: A 855 MET cc_start: 0.6655 (mtm) cc_final: 0.5889 (mtm) REVERT: A 886 GLN cc_start: 0.7822 (mm-40) cc_final: 0.6486 (mp10) REVERT: A 889 ARG cc_start: 0.7730 (tmm160) cc_final: 0.7114 (tmm160) REVERT: A 917 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7395 (mm-30) REVERT: A 919 GLU cc_start: 0.7609 (mp0) cc_final: 0.7177 (mp0) REVERT: C 129 MET cc_start: 0.7209 (ppp) cc_final: 0.6628 (ppp) REVERT: C 157 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8172 (tm-30) outliers start: 40 outliers final: 30 residues processed: 228 average time/residue: 0.2175 time to fit residues: 67.8546 Evaluate side-chains 246 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 30 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 95 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS A 642 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138038 restraints weight = 14996.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.142255 restraints weight = 8219.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144921 restraints weight = 5218.084| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9093 Z= 0.158 Angle : 0.574 9.311 12497 Z= 0.301 Chirality : 0.042 0.265 1426 Planarity : 0.004 0.054 1466 Dihedral : 11.516 119.689 1567 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.93 % Allowed : 19.87 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.57 (0.25), residues: 997 helix: 0.01 (0.25), residues: 437 sheet: -2.59 (0.50), residues: 71 loop : -1.79 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 162 HIS 0.002 0.001 HIS A 133 PHE 0.026 0.001 PHE A 283 TYR 0.019 0.001 TYR A 294 ARG 0.004 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7931 (mttt) cc_final: 0.7243 (mttm) REVERT: A 124 MET cc_start: 0.7555 (tpt) cc_final: 0.7213 (tpt) REVERT: A 150 ASN cc_start: 0.7852 (m110) cc_final: 0.7538 (m110) REVERT: A 249 ARG cc_start: 0.7781 (ttm110) cc_final: 0.7471 (ttm-80) REVERT: A 365 ARG cc_start: 0.7267 (mtt90) cc_final: 0.6995 (mtt90) REVERT: A 380 MET cc_start: 0.7399 (tmm) cc_final: 0.7050 (tmm) REVERT: A 395 CYS cc_start: 0.7414 (m) cc_final: 0.7154 (m) REVERT: A 454 ASP cc_start: 0.7437 (t0) cc_final: 0.7116 (t0) REVERT: A 513 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7963 (ttm-80) REVERT: A 645 CYS cc_start: 0.8116 (m) cc_final: 0.6676 (t) REVERT: A 703 ASN cc_start: 0.7932 (m110) cc_final: 0.7486 (m110) REVERT: A 765 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7848 (t) REVERT: A 782 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6897 (t80) REVERT: A 807 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8270 (pttm) REVERT: A 819 LEU cc_start: 0.8479 (tp) cc_final: 0.7222 (tp) REVERT: A 855 MET cc_start: 0.6632 (mtm) cc_final: 0.5848 (mtm) REVERT: A 886 GLN cc_start: 0.7781 (mm-40) cc_final: 0.6332 (mm-40) REVERT: A 889 ARG cc_start: 0.7693 (tmm160) cc_final: 0.6918 (tmm160) REVERT: A 917 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 919 GLU cc_start: 0.7611 (mp0) cc_final: 0.7190 (mp0) REVERT: C 129 MET cc_start: 0.7135 (ppp) cc_final: 0.6533 (ppp) REVERT: C 157 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8144 (tm-30) outliers start: 35 outliers final: 27 residues processed: 240 average time/residue: 0.2174 time to fit residues: 71.0893 Evaluate side-chains 256 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 2 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A 642 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134390 restraints weight = 15014.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138452 restraints weight = 8194.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141129 restraints weight = 5163.547| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9093 Z= 0.278 Angle : 0.637 10.209 12497 Z= 0.335 Chirality : 0.044 0.240 1426 Planarity : 0.004 0.060 1466 Dihedral : 11.602 120.901 1567 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.83 % Allowed : 20.20 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.57 (0.25), residues: 997 helix: 0.03 (0.25), residues: 435 sheet: -2.73 (0.48), residues: 73 loop : -1.77 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 216 HIS 0.003 0.001 HIS A 133 PHE 0.029 0.002 PHE A 283 TYR 0.018 0.002 TYR A 273 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7957 (mttt) cc_final: 0.7384 (mttm) REVERT: A 86 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.4975 (mt) REVERT: A 124 MET cc_start: 0.7614 (tpt) cc_final: 0.7285 (tpt) REVERT: A 150 ASN cc_start: 0.7954 (m110) cc_final: 0.7648 (m110) REVERT: A 183 ARG cc_start: 0.7773 (ttm170) cc_final: 0.7534 (ttp-170) REVERT: A 365 ARG cc_start: 0.7299 (mtt90) cc_final: 0.7019 (mtt90) REVERT: A 380 MET cc_start: 0.7461 (tmm) cc_final: 0.7231 (tmm) REVERT: A 395 CYS cc_start: 0.7615 (m) cc_final: 0.7353 (m) REVERT: A 438 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8169 (mmtt) REVERT: A 454 ASP cc_start: 0.7554 (t0) cc_final: 0.7257 (t0) REVERT: A 513 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7896 (ttm-80) REVERT: A 541 GLN cc_start: 0.7611 (tp40) cc_final: 0.6914 (tp40) REVERT: A 645 CYS cc_start: 0.8168 (m) cc_final: 0.6661 (t) REVERT: A 668 MET cc_start: 0.7668 (tmm) cc_final: 0.7016 (tmm) REVERT: A 694 PHE cc_start: 0.7735 (t80) cc_final: 0.7498 (t80) REVERT: A 703 ASN cc_start: 0.8160 (m110) cc_final: 0.7745 (m110) REVERT: A 765 CYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7911 (t) REVERT: A 782 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6955 (t80) REVERT: A 783 LYS cc_start: 0.8242 (mmpt) cc_final: 0.7843 (mmpt) REVERT: A 855 MET cc_start: 0.6693 (mtm) cc_final: 0.5923 (mtm) REVERT: A 889 ARG cc_start: 0.7722 (tmm160) cc_final: 0.6989 (tmm160) REVERT: C 157 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8157 (tm-30) outliers start: 43 outliers final: 32 residues processed: 242 average time/residue: 0.2169 time to fit residues: 71.5269 Evaluate side-chains 260 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 68 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 76 optimal weight: 0.0970 chunk 45 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A 572 HIS A 642 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135992 restraints weight = 15317.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140302 restraints weight = 8398.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.143105 restraints weight = 5294.842| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9093 Z= 0.179 Angle : 0.594 10.340 12497 Z= 0.310 Chirality : 0.042 0.212 1426 Planarity : 0.004 0.058 1466 Dihedral : 11.415 116.600 1567 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.93 % Allowed : 21.32 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.41 (0.25), residues: 997 helix: 0.14 (0.25), residues: 440 sheet: -2.54 (0.50), residues: 73 loop : -1.69 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 182 HIS 0.002 0.001 HIS A 133 PHE 0.030 0.001 PHE A 283 TYR 0.015 0.001 TYR A 689 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7793 (mttt) cc_final: 0.7178 (mttm) REVERT: A 86 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.4998 (mt) REVERT: A 124 MET cc_start: 0.7637 (tpt) cc_final: 0.7265 (tpt) REVERT: A 150 ASN cc_start: 0.7935 (m110) cc_final: 0.7601 (m110) REVERT: A 219 PHE cc_start: 0.6062 (m-80) cc_final: 0.5823 (m-80) REVERT: A 365 ARG cc_start: 0.7305 (mtt90) cc_final: 0.7016 (mtt90) REVERT: A 380 MET cc_start: 0.7405 (tmm) cc_final: 0.7126 (tmm) REVERT: A 395 CYS cc_start: 0.7591 (m) cc_final: 0.7326 (m) REVERT: A 438 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8065 (mmtt) REVERT: A 454 ASP cc_start: 0.7528 (t0) cc_final: 0.7305 (t0) REVERT: A 541 GLN cc_start: 0.7599 (tp40) cc_final: 0.6971 (tp40) REVERT: A 645 CYS cc_start: 0.8123 (m) cc_final: 0.6632 (t) REVERT: A 668 MET cc_start: 0.7686 (tmm) cc_final: 0.7110 (tmm) REVERT: A 694 PHE cc_start: 0.7848 (t80) cc_final: 0.7533 (t80) REVERT: A 703 ASN cc_start: 0.7999 (m110) cc_final: 0.7571 (m110) REVERT: A 765 CYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7739 (t) REVERT: A 782 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6918 (t80) REVERT: A 783 LYS cc_start: 0.8197 (mmpt) cc_final: 0.7830 (mmpt) REVERT: A 818 MET cc_start: 0.7479 (ppp) cc_final: 0.6818 (ppp) REVERT: A 855 MET cc_start: 0.6696 (mtm) cc_final: 0.6056 (mtm) REVERT: A 889 ARG cc_start: 0.7716 (tmm160) cc_final: 0.6970 (tmm160) REVERT: C 157 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8111 (tm-30) REVERT: D 3 MET cc_start: 0.7335 (ppp) cc_final: 0.6918 (ppp) REVERT: D 7 LYS cc_start: 0.7796 (mttm) cc_final: 0.7356 (mttp) outliers start: 35 outliers final: 26 residues processed: 241 average time/residue: 0.2082 time to fit residues: 68.5831 Evaluate side-chains 255 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 543 ASN A 572 HIS A 642 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.155779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134577 restraints weight = 15104.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138620 restraints weight = 8254.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141321 restraints weight = 5216.648| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9093 Z= 0.287 Angle : 0.651 9.514 12497 Z= 0.345 Chirality : 0.045 0.220 1426 Planarity : 0.004 0.062 1466 Dihedral : 11.535 117.492 1567 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.15 % Allowed : 21.10 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.47 (0.25), residues: 997 helix: 0.11 (0.25), residues: 439 sheet: -2.55 (0.46), residues: 83 loop : -1.72 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 182 HIS 0.004 0.001 HIS A 133 PHE 0.031 0.002 PHE A 283 TYR 0.023 0.002 TYR C 149 ARG 0.006 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7653 (tpt) cc_final: 0.7322 (tpt) REVERT: A 150 ASN cc_start: 0.7972 (m110) cc_final: 0.7643 (m110) REVERT: A 365 ARG cc_start: 0.7297 (mtt90) cc_final: 0.7008 (mtt90) REVERT: A 380 MET cc_start: 0.7428 (tmm) cc_final: 0.7155 (tmm) REVERT: A 395 CYS cc_start: 0.7623 (m) cc_final: 0.7375 (m) REVERT: A 438 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8180 (mmtt) REVERT: A 454 ASP cc_start: 0.7539 (t0) cc_final: 0.7328 (t0) REVERT: A 541 GLN cc_start: 0.7581 (tp40) cc_final: 0.6814 (tp40) REVERT: A 645 CYS cc_start: 0.8072 (m) cc_final: 0.6644 (t) REVERT: A 668 MET cc_start: 0.7650 (tmm) cc_final: 0.7085 (tmm) REVERT: A 694 PHE cc_start: 0.7849 (t80) cc_final: 0.7471 (t80) REVERT: A 703 ASN cc_start: 0.8143 (m110) cc_final: 0.7758 (m110) REVERT: A 765 CYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7886 (t) REVERT: A 782 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6969 (t80) REVERT: A 783 LYS cc_start: 0.8246 (mmpt) cc_final: 0.7883 (mmpt) REVERT: A 818 MET cc_start: 0.7585 (ppp) cc_final: 0.7039 (ppp) REVERT: A 855 MET cc_start: 0.6691 (mtm) cc_final: 0.6048 (mtm) REVERT: A 889 ARG cc_start: 0.7721 (tmm160) cc_final: 0.6984 (tmm160) REVERT: C 157 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8165 (tm-30) outliers start: 37 outliers final: 32 residues processed: 242 average time/residue: 0.2075 time to fit residues: 68.8223 Evaluate side-chains 258 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A 642 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.159365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.137283 restraints weight = 15078.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141501 restraints weight = 8285.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144358 restraints weight = 5265.708| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9093 Z= 0.167 Angle : 0.601 9.785 12497 Z= 0.313 Chirality : 0.042 0.196 1426 Planarity : 0.004 0.056 1466 Dihedral : 11.313 112.366 1567 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.70 % Allowed : 22.67 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.29 (0.25), residues: 997 helix: 0.24 (0.25), residues: 441 sheet: -2.43 (0.49), residues: 71 loop : -1.64 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 182 HIS 0.002 0.000 HIS A 642 PHE 0.028 0.001 PHE A 283 TYR 0.017 0.001 TYR C 149 ARG 0.007 0.000 ARG A 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7725 (mttt) cc_final: 0.7291 (mttm) REVERT: A 86 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.4896 (mt) REVERT: A 124 MET cc_start: 0.7664 (tpt) cc_final: 0.7271 (tpt) REVERT: A 150 ASN cc_start: 0.7890 (m110) cc_final: 0.7571 (m110) REVERT: A 324 THR cc_start: 0.8197 (p) cc_final: 0.7754 (t) REVERT: A 365 ARG cc_start: 0.7289 (mtt90) cc_final: 0.7015 (mtt90) REVERT: A 380 MET cc_start: 0.7410 (tmm) cc_final: 0.7061 (tmm) REVERT: A 395 CYS cc_start: 0.7670 (m) cc_final: 0.7397 (m) REVERT: A 438 LYS cc_start: 0.8394 (mmtm) cc_final: 0.8045 (mmtt) REVERT: A 454 ASP cc_start: 0.7489 (t0) cc_final: 0.7255 (t0) REVERT: A 484 ASP cc_start: 0.7421 (t70) cc_final: 0.7179 (t0) REVERT: A 541 GLN cc_start: 0.7590 (tp40) cc_final: 0.6519 (tp40) REVERT: A 542 MET cc_start: 0.7565 (mtm) cc_final: 0.7245 (mtt) REVERT: A 645 CYS cc_start: 0.8039 (m) cc_final: 0.6605 (t) REVERT: A 668 MET cc_start: 0.7675 (tmm) cc_final: 0.7008 (tmm) REVERT: A 694 PHE cc_start: 0.7896 (t80) cc_final: 0.7489 (t80) REVERT: A 703 ASN cc_start: 0.7957 (m110) cc_final: 0.7525 (m110) REVERT: A 765 CYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7727 (t) REVERT: A 782 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6894 (t80) REVERT: A 783 LYS cc_start: 0.8159 (mmpt) cc_final: 0.7833 (mmpt) REVERT: A 818 MET cc_start: 0.7463 (ppp) cc_final: 0.6728 (ppp) REVERT: A 842 CYS cc_start: 0.7122 (p) cc_final: 0.6890 (p) REVERT: A 855 MET cc_start: 0.6709 (mtm) cc_final: 0.6009 (mtm) REVERT: A 889 ARG cc_start: 0.7690 (tmm160) cc_final: 0.6967 (tmm160) REVERT: C 157 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8095 (tm-30) outliers start: 33 outliers final: 27 residues processed: 240 average time/residue: 0.2065 time to fit residues: 68.5517 Evaluate side-chains 257 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 642 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135806 restraints weight = 15124.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139902 restraints weight = 8305.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142616 restraints weight = 5239.492| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9093 Z= 0.231 Angle : 0.640 8.572 12497 Z= 0.338 Chirality : 0.043 0.208 1426 Planarity : 0.004 0.060 1466 Dihedral : 11.416 114.249 1567 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.48 % Allowed : 22.78 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.43 (0.25), residues: 997 helix: 0.15 (0.25), residues: 442 sheet: -2.42 (0.45), residues: 81 loop : -1.74 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 216 HIS 0.004 0.001 HIS A 133 PHE 0.031 0.002 PHE A 283 TYR 0.020 0.002 TYR C 149 ARG 0.006 0.000 ARG A 631 =============================================================================== Job complete usr+sys time: 2799.71 seconds wall clock time: 50 minutes 14.65 seconds (3014.65 seconds total)