Starting phenix.real_space_refine on Thu Feb 13 18:23:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l1f_23109/02_2025/7l1f_23109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l1f_23109/02_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_23109/02_2025/7l1f_23109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l1f_23109/02_2025/7l1f_23109.map" model { file = "/net/cci-nas-00/data/ceres_data/7l1f_23109/02_2025/7l1f_23109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l1f_23109/02_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-5592/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: 4.93, per 1000 atoms: 0.56 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: 2.10 Conformation dependent library (CDL) restraints added in 926.0 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: 3.24 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: 2.63 Time building geometry restraints manager: 2.45 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.890 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.910 ------------------------------------------------------------------------------- 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 : 0.999 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: 0.2319 time to fit residues: 78.9840 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 : 0.854 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139220 restraints weight = 14897.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143386 restraints weight = 8075.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146143 restraints weight = 5109.244| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 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 : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7505 (tpt) cc_final: 0.7148 (tpt) REVERT: A 150 ASN cc_start: 0.7907 (m110) cc_final: 0.7581 (m110) REVERT: A 167 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: A 242 MET cc_start: 0.7146 (mtp) cc_final: 0.6811 (mtp) REVERT: A 357 GLN cc_start: 0.6701 (mp10) cc_final: 0.6346 (mp10) REVERT: A 365 ARG cc_start: 0.7269 (mtt90) cc_final: 0.7001 (mtt90) REVERT: A 395 CYS cc_start: 0.7458 (m) cc_final: 0.7248 (m) REVERT: A 454 ASP cc_start: 0.7321 (t0) cc_final: 0.6949 (t0) REVERT: A 661 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7025 (mm-40) REVERT: A 698 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: A 703 ASN cc_start: 0.8142 (m110) cc_final: 0.7679 (m110) REVERT: A 765 CYS cc_start: 0.8536 (t) cc_final: 0.8261 (t) REVERT: A 766 PHE cc_start: 0.8651 (p90) cc_final: 0.8024 (p90) REVERT: A 782 PHE cc_start: 0.7312 (m-80) cc_final: 0.6848 (t80) REVERT: A 815 GLN cc_start: 0.7361 (mm-40) cc_final: 0.7071 (mm110) REVERT: A 855 MET cc_start: 0.6627 (mtm) cc_final: 0.6028 (mtm) REVERT: A 889 ARG cc_start: 0.7607 (tmm160) cc_final: 0.7139 (tmm160) REVERT: A 892 HIS cc_start: 0.7826 (t70) cc_final: 0.7618 (t70) REVERT: A 919 GLU cc_start: 0.7813 (mp0) cc_final: 0.7417 (mp0) REVERT: A 924 MET cc_start: 0.7366 (tpp) cc_final: 0.7017 (tpp) REVERT: C 117 LEU cc_start: 0.8003 (tt) cc_final: 0.7786 (tt) REVERT: C 129 MET cc_start: 0.6947 (ppp) cc_final: 0.6383 (ppp) REVERT: C 157 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 2 LYS cc_start: 0.6643 (pttp) cc_final: 0.6220 (pttm) outliers start: 18 outliers final: 13 residues processed: 242 average time/residue: 0.2327 time to fit residues: 75.5390 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 : 0.873 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 0.0670 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 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: 5.4126 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.158153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135768 restraints weight = 15270.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.139940 restraints weight = 8302.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.142658 restraints weight = 5245.834| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9093 Z= 0.290 Angle : 0.656 7.549 12497 Z= 0.353 Chirality : 0.045 0.347 1426 Planarity : 0.005 0.056 1466 Dihedral : 12.119 128.039 1567 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.03 % Allowed : 14.03 % Favored : 82.94 % 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: -2.44 (0.24), residues: 997 helix: -0.88 (0.23), residues: 436 sheet: -2.76 (0.51), residues: 79 loop : -2.09 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 216 HIS 0.004 0.001 HIS D 36 PHE 0.030 0.002 PHE A 415 TYR 0.021 0.002 TYR A 273 ARG 0.009 0.001 ARG A 249 *********************** 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 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7891 (mttt) cc_final: 0.7589 (mttp) REVERT: A 124 MET cc_start: 0.7572 (tpt) cc_final: 0.7199 (tpt) REVERT: A 150 ASN cc_start: 0.7957 (m110) cc_final: 0.7621 (m110) REVERT: A 183 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7474 (ttp-170) REVERT: A 249 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7404 (ttm-80) REVERT: A 365 ARG cc_start: 0.7258 (mtt90) cc_final: 0.6990 (mtt90) REVERT: A 438 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8088 (mmtt) REVERT: A 454 ASP cc_start: 0.7492 (t0) cc_final: 0.7161 (t0) REVERT: A 703 ASN cc_start: 0.8107 (m110) cc_final: 0.7707 (m110) REVERT: A 765 CYS cc_start: 0.8416 (t) cc_final: 0.8036 (t) REVERT: A 782 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6958 (t80) REVERT: A 807 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8229 (pttm) REVERT: A 819 LEU cc_start: 0.8789 (tp) cc_final: 0.8314 (tp) REVERT: A 855 MET cc_start: 0.6664 (mtm) cc_final: 0.5970 (mtm) REVERT: A 881 PHE cc_start: 0.7703 (t80) cc_final: 0.7475 (t80) REVERT: A 889 ARG cc_start: 0.7708 (tmm160) cc_final: 0.7084 (tmm160) REVERT: A 917 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7344 (mm-30) REVERT: A 919 GLU cc_start: 0.7818 (mp0) cc_final: 0.7304 (mp0) REVERT: A 924 MET cc_start: 0.7311 (tpp) cc_final: 0.6929 (ttm) REVERT: C 129 MET cc_start: 0.6959 (ppp) cc_final: 0.6412 (ppp) REVERT: C 157 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7958 (tm-30) outliers start: 27 outliers final: 24 residues processed: 221 average time/residue: 0.2317 time to fit residues: 69.4171 Evaluate side-chains 236 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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 697 CYS 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 782 PHE 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: 6.9990 chunk 97 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.159514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137011 restraints weight = 15210.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.141166 restraints weight = 8338.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143878 restraints weight = 5312.787| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9093 Z= 0.200 Angle : 0.589 10.763 12497 Z= 0.314 Chirality : 0.042 0.305 1426 Planarity : 0.004 0.050 1466 Dihedral : 11.842 125.460 1567 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.70 % Allowed : 16.05 % Favored : 80.25 % 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: -0.35 (0.25), residues: 435 sheet: -2.50 (0.51), residues: 73 loop : -1.98 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 29 HIS 0.002 0.001 HIS A 133 PHE 0.028 0.001 PHE A 415 TYR 0.020 0.001 TYR C 149 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 251 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7913 (mttt) cc_final: 0.7629 (mttm) REVERT: A 124 MET cc_start: 0.7524 (tpt) cc_final: 0.7228 (tpt) REVERT: A 150 ASN cc_start: 0.7816 (m110) cc_final: 0.7535 (m110) REVERT: A 167 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: A 249 ARG cc_start: 0.7744 (ttm110) cc_final: 0.7409 (ttm-80) REVERT: A 297 ASN cc_start: 0.7924 (p0) cc_final: 0.7647 (p0) REVERT: A 365 ARG cc_start: 0.7262 (mtt90) cc_final: 0.6997 (mtt90) REVERT: A 380 MET cc_start: 0.7350 (tmm) cc_final: 0.7043 (tmm) REVERT: A 438 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8028 (mmtt) REVERT: A 454 ASP cc_start: 0.7460 (t0) cc_final: 0.7129 (t0) REVERT: A 576 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 703 ASN cc_start: 0.8080 (m110) cc_final: 0.7675 (m110) REVERT: A 765 CYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7946 (t) REVERT: A 782 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6947 (t80) REVERT: A 819 LEU cc_start: 0.8628 (tp) cc_final: 0.8419 (tp) REVERT: A 855 MET cc_start: 0.6588 (mtm) cc_final: 0.5896 (mtm) REVERT: A 881 PHE cc_start: 0.7657 (t80) cc_final: 0.7374 (t80) REVERT: A 889 ARG cc_start: 0.7652 (tmm160) cc_final: 0.6930 (tmm160) REVERT: A 917 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7444 (mm-30) REVERT: A 919 GLU cc_start: 0.7888 (mp0) cc_final: 0.7360 (mp0) REVERT: A 924 MET cc_start: 0.7222 (tpp) cc_final: 0.6886 (ttm) REVERT: C 129 MET cc_start: 0.6892 (ppp) cc_final: 0.6370 (ppp) REVERT: C 157 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8075 (tm-30) outliers start: 33 outliers final: 21 residues processed: 228 average time/residue: 0.2348 time to fit residues: 73.0352 Evaluate side-chains 239 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 576 LEU 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 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 C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 2 LYS 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: 10.0000 chunk 32 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.0060 chunk 94 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4007 r_free = 0.4007 target = 0.159189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136829 restraints weight = 15085.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140919 restraints weight = 8251.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143637 restraints weight = 5274.044| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9093 Z= 0.208 Angle : 0.582 6.153 12497 Z= 0.309 Chirality : 0.043 0.291 1426 Planarity : 0.004 0.054 1466 Dihedral : 11.677 123.879 1567 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.38 % Allowed : 17.06 % Favored : 78.56 % 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: -1.72 (0.25), residues: 997 helix: -0.08 (0.25), residues: 437 sheet: -2.63 (0.49), residues: 73 loop : -1.90 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 29 HIS 0.003 0.001 HIS A 133 PHE 0.026 0.002 PHE A 415 TYR 0.019 0.001 TYR C 149 ARG 0.007 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 260 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7947 (mttt) cc_final: 0.7253 (mttm) REVERT: A 124 MET cc_start: 0.7586 (tpt) cc_final: 0.7226 (tpt) REVERT: A 150 ASN cc_start: 0.7869 (m110) cc_final: 0.7556 (m110) REVERT: A 249 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7458 (ttm-80) REVERT: A 297 ASN cc_start: 0.7920 (p0) cc_final: 0.7641 (p0) REVERT: A 365 ARG cc_start: 0.7218 (mtt90) cc_final: 0.6945 (mtt90) REVERT: A 380 MET cc_start: 0.7419 (tmm) cc_final: 0.7154 (tmm) REVERT: A 438 LYS cc_start: 0.8429 (mmtm) cc_final: 0.8082 (mmtt) REVERT: A 454 ASP cc_start: 0.7458 (t0) cc_final: 0.7151 (t0) REVERT: A 694 PHE cc_start: 0.7725 (t80) cc_final: 0.7365 (t80) REVERT: A 703 ASN cc_start: 0.8086 (m110) cc_final: 0.7701 (m110) REVERT: A 765 CYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7920 (t) REVERT: A 782 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 819 LEU cc_start: 0.8573 (tp) cc_final: 0.7288 (tp) REVERT: A 855 MET cc_start: 0.6640 (mtm) cc_final: 0.5885 (mtm) REVERT: A 881 PHE cc_start: 0.7654 (t80) cc_final: 0.7372 (t80) REVERT: A 889 ARG cc_start: 0.7708 (tmm160) cc_final: 0.6964 (tmm160) REVERT: A 917 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7352 (mm-30) REVERT: A 919 GLU cc_start: 0.7676 (mp0) cc_final: 0.7226 (mp0) REVERT: C 129 MET cc_start: 0.6914 (ppp) cc_final: 0.6347 (ppp) REVERT: C 157 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8102 (tm-30) REVERT: D 23 GLU cc_start: 0.6905 (tt0) cc_final: 0.6696 (tt0) outliers start: 39 outliers final: 28 residues processed: 233 average time/residue: 0.2370 time to fit residues: 74.6097 Evaluate side-chains 247 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 479 TYR 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 673 LEU Chi-restraints excluded: chain A residue 697 CYS 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 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 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: 0.8980 chunk 26 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.163017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140428 restraints weight = 15090.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144641 restraints weight = 8293.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147403 restraints weight = 5279.752| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9093 Z= 0.145 Angle : 0.568 10.790 12497 Z= 0.292 Chirality : 0.040 0.250 1426 Planarity : 0.004 0.050 1466 Dihedral : 11.406 119.882 1567 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.48 % Allowed : 19.08 % Favored : 77.44 % 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: -1.39 (0.25), residues: 997 helix: 0.18 (0.25), residues: 438 sheet: -2.06 (0.53), residues: 69 loop : -1.80 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 268 HIS 0.002 0.001 HIS A 295 PHE 0.022 0.001 PHE A 415 TYR 0.020 0.001 TYR A 689 ARG 0.007 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 253 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7791 (mttt) cc_final: 0.7108 (mttm) REVERT: A 124 MET cc_start: 0.7532 (tpt) cc_final: 0.7158 (tpt) REVERT: A 150 ASN cc_start: 0.7799 (m110) cc_final: 0.7476 (m110) REVERT: A 249 ARG cc_start: 0.7743 (ttm110) cc_final: 0.7448 (ttm-80) REVERT: A 297 ASN cc_start: 0.7865 (p0) cc_final: 0.7488 (p0) REVERT: A 365 ARG cc_start: 0.7263 (mtt90) cc_final: 0.6993 (mtt90) REVERT: A 380 MET cc_start: 0.7397 (tmm) cc_final: 0.7135 (tmm) REVERT: A 454 ASP cc_start: 0.7357 (t0) cc_final: 0.7068 (t0) REVERT: A 673 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7894 (tp) REVERT: A 694 PHE cc_start: 0.7669 (t80) cc_final: 0.7305 (t80) REVERT: A 703 ASN cc_start: 0.7917 (m110) cc_final: 0.7526 (m110) REVERT: A 765 CYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7628 (t) REVERT: A 782 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6871 (t80) REVERT: A 842 CYS cc_start: 0.7085 (p) cc_final: 0.6847 (p) REVERT: A 855 MET cc_start: 0.6515 (mtm) cc_final: 0.5781 (mtm) REVERT: A 889 ARG cc_start: 0.7675 (tmm160) cc_final: 0.6989 (tmm160) REVERT: A 917 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7387 (mm-30) REVERT: A 919 GLU cc_start: 0.7663 (mp0) cc_final: 0.7235 (mp0) REVERT: C 129 MET cc_start: 0.6855 (ppp) cc_final: 0.6373 (ppp) REVERT: C 157 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8082 (tm-30) outliers start: 31 outliers final: 19 residues processed: 232 average time/residue: 0.2184 time to fit residues: 69.7615 Evaluate side-chains 239 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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 473 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 556 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 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: 10.0000 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.154610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133395 restraints weight = 15045.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.137372 restraints weight = 8258.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140053 restraints weight = 5244.132| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 : 0.006 0.038 9093 Z= 0.352 Angle : 0.684 9.002 12497 Z= 0.364 Chirality : 0.046 0.259 1426 Planarity : 0.005 0.065 1466 Dihedral : 11.664 122.946 1567 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.15 % Allowed : 19.75 % Favored : 76.09 % 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: -1.60 (0.25), residues: 997 helix: 0.02 (0.25), residues: 438 sheet: -2.48 (0.50), residues: 73 loop : -1.85 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 216 HIS 0.005 0.001 HIS A 133 PHE 0.025 0.002 PHE A 415 TYR 0.025 0.002 TYR A 237 ARG 0.007 0.001 ARG A 513 *********************** 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 254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7974 (mttt) cc_final: 0.7253 (mttm) REVERT: A 86 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.4847 (mt) REVERT: A 124 MET cc_start: 0.7647 (tpt) cc_final: 0.7318 (tpt) REVERT: A 150 ASN cc_start: 0.7984 (m110) cc_final: 0.7640 (m110) REVERT: A 297 ASN cc_start: 0.7961 (p0) cc_final: 0.7630 (p0) REVERT: A 365 ARG cc_start: 0.7285 (mtt90) cc_final: 0.7002 (mtt90) REVERT: A 380 MET cc_start: 0.7453 (tmm) cc_final: 0.7145 (tmm) REVERT: A 438 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8145 (mmtt) REVERT: A 454 ASP cc_start: 0.7574 (t0) cc_final: 0.7276 (t0) REVERT: A 694 PHE cc_start: 0.7777 (t80) cc_final: 0.7537 (t80) REVERT: A 703 ASN cc_start: 0.8210 (m110) cc_final: 0.7827 (m110) REVERT: A 765 CYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7938 (t) REVERT: A 782 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6911 (t80) REVERT: A 783 LYS cc_start: 0.8275 (mmpt) cc_final: 0.7884 (mmpt) REVERT: A 818 MET cc_start: 0.7386 (ppp) cc_final: 0.6581 (ppp) REVERT: A 819 LEU cc_start: 0.8213 (tp) cc_final: 0.7334 (mt) REVERT: A 855 MET cc_start: 0.6683 (mtm) cc_final: 0.6062 (mtm) REVERT: A 889 ARG cc_start: 0.7736 (tmm160) cc_final: 0.7057 (tmm160) REVERT: C 129 MET cc_start: 0.6999 (ppp) cc_final: 0.6317 (ppp) REVERT: C 157 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8160 (tm-30) outliers start: 37 outliers final: 23 residues processed: 230 average time/residue: 0.2149 time to fit residues: 67.3628 Evaluate side-chains 240 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 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 615 MET Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 756 MET 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: 9.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.8504 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.157903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136406 restraints weight = 15312.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140531 restraints weight = 8295.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143251 restraints weight = 5228.698| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9093 Z= 0.190 Angle : 0.606 9.497 12497 Z= 0.315 Chirality : 0.042 0.212 1426 Planarity : 0.004 0.059 1466 Dihedral : 11.465 117.465 1567 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.59 % Allowed : 21.32 % Favored : 75.08 % 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: 0.12 (0.25), residues: 442 sheet: -2.32 (0.51), residues: 71 loop : -1.75 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 216 HIS 0.002 0.001 HIS A 872 PHE 0.024 0.001 PHE A 415 TYR 0.030 0.001 TYR A 294 ARG 0.007 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 250 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7817 (mttt) cc_final: 0.6985 (mttm) REVERT: A 124 MET cc_start: 0.7638 (tpt) cc_final: 0.7274 (tpt) REVERT: A 150 ASN cc_start: 0.7877 (m110) cc_final: 0.7548 (m110) REVERT: A 271 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5691 (mp) REVERT: A 297 ASN cc_start: 0.7779 (p0) cc_final: 0.7383 (p0) REVERT: A 365 ARG cc_start: 0.7275 (mtt90) cc_final: 0.6996 (mtt90) REVERT: A 380 MET cc_start: 0.7422 (tmm) cc_final: 0.7102 (tmm) REVERT: A 454 ASP cc_start: 0.7516 (t0) cc_final: 0.7293 (t0) REVERT: A 694 PHE cc_start: 0.7823 (t80) cc_final: 0.7485 (t80) REVERT: A 703 ASN cc_start: 0.8091 (m110) cc_final: 0.7665 (m110) REVERT: A 765 CYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7756 (t) REVERT: A 782 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6908 (t80) REVERT: A 783 LYS cc_start: 0.8184 (mmpt) cc_final: 0.7807 (mmpt) REVERT: A 818 MET cc_start: 0.7498 (ppp) cc_final: 0.6732 (ppp) REVERT: A 842 CYS cc_start: 0.7089 (p) cc_final: 0.6805 (p) REVERT: A 855 MET cc_start: 0.6619 (mtm) cc_final: 0.5979 (mtm) REVERT: A 889 ARG cc_start: 0.7737 (tmm160) cc_final: 0.7040 (tmm160) REVERT: C 129 MET cc_start: 0.6901 (ppp) cc_final: 0.6305 (ppp) REVERT: C 157 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 7 LYS cc_start: 0.7725 (mttm) cc_final: 0.7330 (mttp) outliers start: 32 outliers final: 27 residues processed: 230 average time/residue: 0.2143 time to fit residues: 67.4540 Evaluate side-chains 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 271 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 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 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 2 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A 572 HIS A 642 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.154930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133647 restraints weight = 15155.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137701 restraints weight = 8319.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140421 restraints weight = 5257.158| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9093 Z= 0.331 Angle : 0.677 8.454 12497 Z= 0.359 Chirality : 0.046 0.222 1426 Planarity : 0.005 0.064 1466 Dihedral : 11.629 118.171 1567 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.93 % Allowed : 21.10 % 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: -1.51 (0.25), residues: 997 helix: 0.05 (0.25), residues: 438 sheet: -2.53 (0.50), residues: 72 loop : -1.74 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 216 HIS 0.010 0.001 HIS A 572 PHE 0.035 0.002 PHE A 283 TYR 0.034 0.002 TYR A 294 ARG 0.005 0.001 ARG A 569 *********************** 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 251 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7886 (mttt) cc_final: 0.7185 (mttm) REVERT: A 86 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.4824 (mt) REVERT: A 124 MET cc_start: 0.7659 (tpt) cc_final: 0.7041 (tpt) REVERT: A 150 ASN cc_start: 0.7965 (m110) cc_final: 0.7620 (m110) REVERT: A 297 ASN cc_start: 0.7767 (p0) cc_final: 0.7382 (p0) REVERT: A 365 ARG cc_start: 0.7295 (mtt90) cc_final: 0.7006 (mtt90) REVERT: A 380 MET cc_start: 0.7461 (tmm) cc_final: 0.7149 (tmm) REVERT: A 438 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8084 (mmtt) REVERT: A 454 ASP cc_start: 0.7572 (t0) cc_final: 0.7371 (t0) REVERT: A 668 MET cc_start: 0.7704 (tmm) cc_final: 0.7136 (tmm) REVERT: A 694 PHE cc_start: 0.7889 (t80) cc_final: 0.7481 (t80) REVERT: A 703 ASN cc_start: 0.8177 (m110) cc_final: 0.7778 (m110) REVERT: A 765 CYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7951 (t) REVERT: A 782 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.6973 (t80) REVERT: A 783 LYS cc_start: 0.8233 (mmpt) cc_final: 0.7881 (mmpt) REVERT: A 818 MET cc_start: 0.7593 (ppp) cc_final: 0.6897 (ppp) REVERT: A 855 MET cc_start: 0.6682 (mtm) cc_final: 0.6020 (mtm) REVERT: A 889 ARG cc_start: 0.7736 (tmm160) cc_final: 0.7053 (tmm160) REVERT: C 129 MET cc_start: 0.6983 (ppp) cc_final: 0.6292 (ppp) REVERT: C 157 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8175 (tm-30) outliers start: 35 outliers final: 26 residues processed: 230 average time/residue: 0.2145 time to fit residues: 67.5088 Evaluate side-chains 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 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 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 2 LYS 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: 6.9990 chunk 87 optimal weight: 0.0270 chunk 97 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN 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 = 0.3995 r_free = 0.3995 target = 0.158568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.137310 restraints weight = 15018.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141417 restraints weight = 8199.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144159 restraints weight = 5169.935| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3269 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= 0.169 Angle : 0.608 8.509 12497 Z= 0.315 Chirality : 0.042 0.201 1426 Planarity : 0.004 0.057 1466 Dihedral : 11.375 113.027 1567 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.37 % Allowed : 21.55 % Favored : 75.08 % 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: -1.27 (0.25), residues: 997 helix: 0.25 (0.25), residues: 439 sheet: -1.93 (0.57), residues: 61 loop : -1.73 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 182 HIS 0.002 0.001 HIS A 642 PHE 0.034 0.001 PHE A 283 TYR 0.033 0.001 TYR A 294 ARG 0.005 0.000 ARG A 631 ********************** 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 254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7867 (mttt) cc_final: 0.7190 (mttm) REVERT: A 86 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.4979 (mt) REVERT: A 124 MET cc_start: 0.7643 (tpt) cc_final: 0.7293 (tpt) REVERT: A 150 ASN cc_start: 0.7858 (m110) cc_final: 0.7521 (m110) REVERT: A 297 ASN cc_start: 0.7756 (p0) cc_final: 0.7358 (p0) REVERT: A 324 THR cc_start: 0.8251 (p) cc_final: 0.7813 (t) REVERT: A 365 ARG cc_start: 0.7267 (mtt90) cc_final: 0.6982 (mtt90) REVERT: A 380 MET cc_start: 0.7409 (tmm) cc_final: 0.7069 (tmm) REVERT: A 395 CYS cc_start: 0.7546 (m) cc_final: 0.7252 (m) REVERT: A 454 ASP cc_start: 0.7468 (t0) cc_final: 0.7239 (t0) REVERT: A 645 CYS cc_start: 0.7977 (m) cc_final: 0.6582 (t) REVERT: A 694 PHE cc_start: 0.7830 (t80) cc_final: 0.7424 (t80) REVERT: A 703 ASN cc_start: 0.7948 (m110) cc_final: 0.7520 (m110) REVERT: A 765 CYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7857 (t) REVERT: A 782 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.6898 (t80) REVERT: A 783 LYS cc_start: 0.8161 (mmpt) cc_final: 0.7792 (mmpt) REVERT: A 818 MET cc_start: 0.7498 (ppp) cc_final: 0.6708 (ppp) REVERT: A 842 CYS cc_start: 0.7088 (p) cc_final: 0.6851 (p) REVERT: A 855 MET cc_start: 0.6598 (mtm) cc_final: 0.5943 (mtm) REVERT: A 889 ARG cc_start: 0.7711 (tmm160) cc_final: 0.7041 (tmm160) REVERT: C 129 MET cc_start: 0.6871 (ppp) cc_final: 0.6282 (ppp) REVERT: C 157 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8115 (tm-30) REVERT: D 3 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6905 (ppp) REVERT: D 7 LYS cc_start: 0.7782 (mttm) cc_final: 0.7386 (mttp) outliers start: 30 outliers final: 23 residues processed: 236 average time/residue: 0.2024 time to fit residues: 66.2524 Evaluate side-chains 248 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 435 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 541 GLN 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 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 D residue 2 LYS Chi-restraints excluded: chain D residue 3 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 543 ASN 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 = 0.3992 r_free = 0.3992 target = 0.158414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137181 restraints weight = 15133.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141290 restraints weight = 8292.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144006 restraints weight = 5233.661| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9093 Z= 0.190 Angle : 0.625 9.436 12497 Z= 0.328 Chirality : 0.042 0.191 1426 Planarity : 0.004 0.057 1466 Dihedral : 11.357 113.517 1567 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.37 % Allowed : 22.33 % Favored : 74.30 % 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: -1.25 (0.25), residues: 997 helix: 0.30 (0.25), residues: 437 sheet: -1.91 (0.57), residues: 61 loop : -1.74 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 182 HIS 0.003 0.001 HIS A 133 PHE 0.034 0.001 PHE A 283 TYR 0.033 0.001 TYR A 294 ARG 0.007 0.000 ARG A 331 =============================================================================== Job complete usr+sys time: 2594.31 seconds wall clock time: 47 minutes 31.07 seconds (2851.07 seconds total)