Starting phenix.real_space_refine on Fri Sep 11 21:40:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dok_30795/09_2026/7dok_30795.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dok_30795/09_2026/7dok_30795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dok_30795/09_2026/7dok_30795.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dok_30795/09_2026/7dok_30795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dok_30795/09_2026/7dok_30795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dok_30795/09_2026/7dok_30795.map" model { file = "/net/cci-nas-00/data/ceres_data/7dok_30795/09_2026/7dok_30795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dok_30795/09_2026/7dok_30795.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 49 5.49 5 Mg 4 5.21 5 S 81 5.16 5 C 7141 2.51 5 N 1942 2.21 5 O 2315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11534 Number of models: 1 Model: "" Number of chains: 8 Chain: "P" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNAv2': 20} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain: "T" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 499 Classifications: {'RNAv2': 24} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 15} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 7457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7457 Classifications: {'peptide': 925} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 894} Chain: "B" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1214 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 149} Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 530 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "G" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1360 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain breaks: 1 Chain: "P" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'HCU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 25 Unusual residues: {' MG': 3, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 7, 'water': 2} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3367 SG CYS A 301 90.773 66.447 46.517 1.00 23.11 S ATOM 3408 SG CYS A 306 90.854 65.667 42.318 1.00 23.19 S ATOM 3440 SG CYS A 310 94.122 65.636 44.859 1.00 20.66 S ATOM 4848 SG CYS A 487 72.617 61.166 54.936 1.00 29.89 S ATOM 6101 SG CYS A 645 71.622 60.925 50.803 1.00 32.78 S ATOM 6107 SG CYS A 646 74.723 63.422 52.381 1.00 31.19 S Time building chain proxies: 2.46, per 1000 atoms: 0.21 Number of scatterers: 11534 At special positions: 0 Unit cell: (150.729, 94.072, 131.487, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 81 16.00 P 49 15.00 Mg 4 11.99 O 2315 8.00 N 1942 7.00 C 7141 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 452.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 52.5% alpha, 15.6% beta 20 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.533A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.675A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.532A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.526A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.078A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.382A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 259 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.504A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.700A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.407A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.535A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.772A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.505A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.828A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 582 removed outlier: 3.688A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.556A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.851A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 866 removed outlier: 3.735A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.556A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.206A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'B' and resid 38 through 98 removed outlier: 3.584A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.734A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.740A pdb=" N ALA B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.826A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.800A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 47 through 61 removed outlier: 3.676A pdb=" N LYS C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.776A pdb=" N ALA G 13 " --> pdb=" O LEU G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 99 removed outlier: 3.657A pdb=" N LYS G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER G 41 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR G 84 " --> pdb=" O ARG G 80 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 113 removed outlier: 3.820A pdb=" N ILE G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.202A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.549A pdb=" N ILE A 223 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.367A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.367A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.463A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'G' and resid 128 through 132 removed outlier: 6.205A pdb=" N ILE G 185 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL G 159 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR G 187 " --> pdb=" O GLN G 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 128 through 132 removed outlier: 6.205A pdb=" N ILE G 185 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL G 159 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR G 187 " --> pdb=" O GLN G 157 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL G 159 " --> pdb=" O VAL G 167 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2573 1.33 - 1.45: 2813 1.45 - 1.57: 6254 1.57 - 1.69: 90 1.69 - 1.81: 127 Bond restraints: 11857 Sorted by residual: bond pdb=" O3 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.668 1.429 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C9 HCU P1201 " pdb=" O3 HCU P1201 " ideal model delta sigma weight residual 1.417 1.222 0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" O4 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.519 1.338 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " ideal model delta sigma weight residual 1.535 1.375 0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C1 HCU P1201 " pdb=" O1 HCU P1201 " ideal model delta sigma weight residual 1.243 1.401 -0.158 2.00e-02 2.50e+03 6.27e+01 ... (remaining 11852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 16172 3.96 - 7.93: 88 7.93 - 11.89: 12 11.89 - 15.86: 1 15.86 - 19.82: 2 Bond angle restraints: 16275 Sorted by residual: angle pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " pdb=" C9 HCU P1201 " ideal model delta sigma weight residual 112.97 132.79 -19.82 3.00e+00 1.11e-01 4.37e+01 angle pdb=" C2' G P 8 " pdb=" C1' G P 8 " pdb=" N9 G P 8 " ideal model delta sigma weight residual 112.40 101.41 10.99 2.00e+00 2.50e-01 3.02e+01 angle pdb=" C9 HCU P1201 " pdb=" O3 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 121.95 137.98 -16.03 3.00e+00 1.11e-01 2.86e+01 angle pdb=" N THR A 26 " pdb=" CA THR A 26 " pdb=" C THR A 26 " ideal model delta sigma weight residual 112.92 107.62 5.30 1.23e+00 6.61e-01 1.86e+01 angle pdb=" C6 HCU P1201 " pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " ideal model delta sigma weight residual 116.16 103.77 12.39 3.00e+00 1.11e-01 1.70e+01 ... (remaining 16270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 6496 21.47 - 42.94: 458 42.94 - 64.41: 52 64.41 - 85.89: 8 85.89 - 107.36: 2 Dihedral angle restraints: 7016 sinusoidal: 3084 harmonic: 3932 Sorted by residual: dihedral pdb=" C4' U P 7 " pdb=" C3' U P 7 " pdb=" C2' U P 7 " pdb=" C1' U P 7 " ideal model delta sinusoidal sigma weight residual 36.34 3.53 32.82 1 3.10e+00 1.04e-01 1.59e+02 dihedral pdb=" C4' G P 8 " pdb=" C3' G P 8 " pdb=" C2' G P 8 " pdb=" C1' G P 8 " ideal model delta sinusoidal sigma weight residual 36.34 7.41 28.93 1 3.10e+00 1.04e-01 1.25e+02 dihedral pdb=" O4' U P 7 " pdb=" C2' U P 7 " pdb=" C1' U P 7 " pdb=" C3' U P 7 " ideal model delta sinusoidal sigma weight residual 25.59 -6.50 32.09 3 3.80e+00 6.93e-02 8.19e+01 ... (remaining 7013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 1860 0.287 - 0.573: 1 0.573 - 0.860: 0 0.860 - 1.146: 0 1.146 - 1.433: 1 Chirality restraints: 1862 Sorted by residual: chirality pdb=" C8 HCU P1201 " pdb=" C10 HCU P1201 " pdb=" C7 HCU P1201 " pdb=" C9 HCU P1201 " both_signs ideal model delta sigma weight residual False -2.60 -1.16 -1.43 2.00e-01 2.50e+01 5.13e+01 chirality pdb=" C3' G P 8 " pdb=" C4' G P 8 " pdb=" O3' G P 8 " pdb=" C2' G P 8 " both_signs ideal model delta sigma weight residual False -2.50 -2.21 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C2' U P 7 " pdb=" C3' U P 7 " pdb=" O2' U P 7 " pdb=" C1' U P 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1859 not shown) Planarity restraints: 1915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 155 " 0.021 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ASP A 155 " -0.070 2.00e-02 2.50e+03 pdb=" O ASP A 155 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR A 156 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G P 8 " 0.011 2.00e-02 2.50e+03 2.18e-02 1.43e+01 pdb=" N9 G P 8 " -0.056 2.00e-02 2.50e+03 pdb=" C8 G P 8 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G P 8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G P 8 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G P 8 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G P 8 " 0.000 2.00e-02 2.50e+03 pdb=" N1 G P 8 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G P 8 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G P 8 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G P 8 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G P 8 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.044 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO B 178 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.037 5.00e-02 4.00e+02 ... (remaining 1912 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 19 2.34 - 2.98: 5163 2.98 - 3.62: 17185 3.62 - 4.26: 28451 4.26 - 4.90: 45694 Nonbonded interactions: 96512 Sorted by model distance: nonbonded pdb=" O4 POP A1003 " pdb=" O HOH A1101 " model vdw 1.695 3.040 nonbonded pdb="MG MG A1005 " pdb=" O6 POP A1007 " model vdw 1.731 2.170 nonbonded pdb="MG MG A1006 " pdb=" O2 POP A1007 " model vdw 1.950 2.170 nonbonded pdb=" O PHE A 77 " pdb=" OE1 GLN A 81 " model vdw 2.035 3.040 nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1005 " model vdw 2.052 2.170 ... (remaining 96507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'G' and resid 37 through 191) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.150 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.010 0.433 11865 Z= 0.515 Angle : 1.043 19.823 16278 Z= 0.633 Chirality : 0.079 1.433 1862 Planarity : 0.006 0.065 1915 Dihedral : 13.931 107.357 4470 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.60 % Allowed : 4.29 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.20), residues: 1313 helix: -1.65 (0.17), residues: 651 sheet: -0.82 (0.41), residues: 148 loop : -1.51 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.022 0.002 TYR A 831 PHE 0.025 0.003 PHE C 49 TRP 0.015 0.002 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00842 / 0.49 (11857) covalent geometry : angle 1.03709 / 0.63 (16275) hydrogen bonds : bond 0.17792 / 9.02 ( 593) hydrogen bonds : angle 6.81290 / 2.71 ( 1691) metal coordination : bond 0.21484 / 10.74 ( 7) metal coordination : angle 8.00758 / 2.67 ( 3) Misc. bond : bond 0.05228 / 2.61 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 198 time to evaluate : 0.459 Fit side-chains REVERT: A 72 VAL cc_start: 0.7956 (m) cc_final: 0.7654 (t) REVERT: A 924 MET cc_start: 0.8554 (mmm) cc_final: 0.8286 (mmt) REVERT: B 67 MET cc_start: 0.6169 (ptp) cc_final: 0.5968 (ptp) REVERT: B 171 GLU cc_start: 0.7385 (tt0) cc_final: 0.7078 (tt0) REVERT: C 23 GLU cc_start: 0.8336 (pt0) cc_final: 0.8080 (pt0) REVERT: G 55 MET cc_start: 0.7340 (mtp) cc_final: 0.6286 (pp-130) REVERT: G 59 LEU cc_start: 0.8204 (mt) cc_final: 0.7927 (mp) REVERT: G 75 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7610 (mmm-85) outliers start: 7 outliers final: 2 residues processed: 204 average time/residue: 0.5316 time to fit residues: 118.7026 Evaluate side-chains 143 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 141 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 906 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 ASN A 75 HIS A 117 GLN A 360 ASN A 403 ASN A 691 ASN A 773 GLN B 105 ASN B 136 ASN B 158 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 100 ASN G 179 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.140982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100670 restraints weight = 15990.884| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.69 r_work: 0.3092 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11865 Z= 0.168 Angle : 0.596 6.377 16278 Z= 0.306 Chirality : 0.045 0.210 1862 Planarity : 0.004 0.050 1915 Dihedral : 8.783 87.923 1983 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.83 % Allowed : 10.29 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.22), residues: 1313 helix: -0.07 (0.19), residues: 644 sheet: -0.71 (0.42), residues: 140 loop : -0.69 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.019 0.002 TYR A 87 PHE 0.016 0.002 PHE A 652 TRP 0.013 0.002 TRP A 509 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (11857) covalent geometry : angle 0.59510 / 0.31 (16275) hydrogen bonds : bond 0.05021 / 2.58 ( 593) hydrogen bonds : angle 4.52834 / 1.82 ( 1691) metal coordination : bond 0.01678 / 0.84 ( 7) metal coordination : angle 2.59383 / 0.86 ( 3) Misc. bond : bond 0.00089 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7856 (p0) cc_final: 0.7652 (p0) REVERT: A 360 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6659 (p0) REVERT: A 633 MET cc_start: 0.8563 (tmm) cc_final: 0.8103 (ttp) REVERT: A 714 LYS cc_start: 0.8527 (mmmm) cc_final: 0.7818 (mtpt) REVERT: A 750 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8517 (mmm-85) REVERT: A 755 MET cc_start: 0.9487 (mtm) cc_final: 0.9281 (mtm) REVERT: A 902 MET cc_start: 0.6456 (mtp) cc_final: 0.6209 (mtt) REVERT: A 924 MET cc_start: 0.9071 (mmm) cc_final: 0.8635 (mmt) REVERT: B 95 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6759 (pp) REVERT: B 171 GLU cc_start: 0.7620 (tt0) cc_final: 0.7345 (tt0) REVERT: C 23 GLU cc_start: 0.8952 (pt0) cc_final: 0.8718 (pt0) REVERT: G 55 MET cc_start: 0.7435 (mtp) cc_final: 0.6280 (pp-130) REVERT: G 59 LEU cc_start: 0.8124 (mt) cc_final: 0.7782 (mp) REVERT: G 99 ASP cc_start: 0.7278 (t0) cc_final: 0.6871 (OUTLIER) REVERT: G 136 ASN cc_start: 0.6640 (p0) cc_final: 0.6242 (p0) REVERT: G 174 MET cc_start: 0.6495 (tpt) cc_final: 0.6206 (mmm) outliers start: 33 outliers final: 17 residues processed: 169 average time/residue: 0.5042 time to fit residues: 93.8521 Evaluate side-chains 156 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 360 ASN A 403 ASN B 136 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.142696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102445 restraints weight = 16060.481| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.71 r_work: 0.3118 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11865 Z= 0.111 Angle : 0.539 9.887 16278 Z= 0.272 Chirality : 0.043 0.254 1862 Planarity : 0.003 0.045 1915 Dihedral : 8.353 70.209 1980 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.92 % Allowed : 12.09 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1313 helix: 0.49 (0.20), residues: 658 sheet: -0.50 (0.41), residues: 136 loop : -0.53 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 75 TYR 0.016 0.001 TYR A 87 PHE 0.014 0.001 PHE A 652 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (11857) covalent geometry : angle 0.53879 / 0.27 (16275) hydrogen bonds : bond 0.04110 / 2.11 ( 593) hydrogen bonds : angle 4.14713 / 1.67 ( 1691) metal coordination : bond 0.00867 / 0.43 ( 7) metal coordination : angle 1.88901 / 0.63 ( 3) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.448 Fit side-chains REVERT: A 57 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6086 (tm-30) REVERT: A 153 ASP cc_start: 0.7773 (p0) cc_final: 0.7530 (p0) REVERT: A 360 ASN cc_start: 0.6749 (OUTLIER) cc_final: 0.6283 (p0) REVERT: A 372 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7950 (mp) REVERT: A 633 MET cc_start: 0.8515 (tmm) cc_final: 0.8059 (ttp) REVERT: A 892 HIS cc_start: 0.7846 (t-90) cc_final: 0.7595 (t70) REVERT: A 902 MET cc_start: 0.6346 (mtp) cc_final: 0.6095 (mtt) REVERT: A 924 MET cc_start: 0.9022 (mmm) cc_final: 0.8727 (mmt) REVERT: B 55 MET cc_start: 0.2991 (mmt) cc_final: 0.2623 (mtm) REVERT: B 95 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6646 (pp) REVERT: B 171 GLU cc_start: 0.7721 (tt0) cc_final: 0.7388 (tt0) REVERT: C 23 GLU cc_start: 0.8891 (pt0) cc_final: 0.8677 (pt0) REVERT: G 55 MET cc_start: 0.7394 (mtp) cc_final: 0.6255 (pp-130) REVERT: G 59 LEU cc_start: 0.8116 (mt) cc_final: 0.7744 (mp) REVERT: G 99 ASP cc_start: 0.7231 (t0) cc_final: 0.6810 (t0) REVERT: G 129 MET cc_start: 0.8074 (mpp) cc_final: 0.7855 (mpp) REVERT: G 136 ASN cc_start: 0.6452 (p0) cc_final: 0.6168 (p0) REVERT: G 161 ASP cc_start: 0.6511 (t0) cc_final: 0.6203 (t0) outliers start: 34 outliers final: 15 residues processed: 168 average time/residue: 0.5075 time to fit residues: 93.6039 Evaluate side-chains 157 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 160 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 403 ASN A 541 GLN A 642 HIS B 88 GLN B 105 ASN B 136 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098613 restraints weight = 16076.762| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.69 r_work: 0.3065 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11865 Z= 0.245 Angle : 0.627 9.107 16278 Z= 0.314 Chirality : 0.047 0.241 1862 Planarity : 0.004 0.045 1915 Dihedral : 8.428 69.476 1980 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.95 % Allowed : 12.86 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1313 helix: 0.51 (0.20), residues: 656 sheet: -0.63 (0.40), residues: 145 loop : -0.56 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 365 TYR 0.017 0.002 TYR A 87 PHE 0.016 0.002 PHE A 652 TRP 0.014 0.002 TRP A 290 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.25 (11857) covalent geometry : angle 0.62613 / 0.31 (16275) hydrogen bonds : bond 0.05099 / 2.64 ( 593) hydrogen bonds : angle 4.24912 / 1.71 ( 1691) metal coordination : bond 0.01646 / 0.82 ( 7) metal coordination : angle 2.33844 / 0.78 ( 3) Misc. bond : bond 0.00180 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7858 (p0) cc_final: 0.7589 (p0) REVERT: A 360 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6243 (p0) REVERT: A 436 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: A 633 MET cc_start: 0.8596 (tmm) cc_final: 0.8102 (ttp) REVERT: A 758 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.8520 (tp) REVERT: A 892 HIS cc_start: 0.7880 (t-90) cc_final: 0.7641 (t-90) REVERT: A 902 MET cc_start: 0.6264 (mtp) cc_final: 0.5686 (ptm) REVERT: A 924 MET cc_start: 0.9125 (mmm) cc_final: 0.8727 (mmt) REVERT: B 95 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6697 (pp) REVERT: B 171 GLU cc_start: 0.7747 (tt0) cc_final: 0.7394 (tt0) REVERT: C 23 GLU cc_start: 0.8888 (pt0) cc_final: 0.8668 (pt0) REVERT: G 55 MET cc_start: 0.7378 (mtp) cc_final: 0.6361 (pp-130) REVERT: G 99 ASP cc_start: 0.7333 (t0) cc_final: 0.6926 (t0) REVERT: G 136 ASN cc_start: 0.6445 (p0) cc_final: 0.6238 (p0) REVERT: G 174 MET cc_start: 0.6380 (tpt) cc_final: 0.6164 (mmm) outliers start: 46 outliers final: 21 residues processed: 170 average time/residue: 0.4933 time to fit residues: 92.0453 Evaluate side-chains 151 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 160 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 360 ASN A 403 ASN A 543 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 136 ASN B 158 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102335 restraints weight = 16002.045| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.88 r_work: 0.3094 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11865 Z= 0.110 Angle : 0.539 8.289 16278 Z= 0.269 Chirality : 0.043 0.263 1862 Planarity : 0.003 0.045 1915 Dihedral : 8.241 55.799 1980 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.57 % Allowed : 15.27 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.23), residues: 1313 helix: 0.81 (0.21), residues: 662 sheet: -0.56 (0.40), residues: 143 loop : -0.39 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 365 TYR 0.016 0.001 TYR A 87 PHE 0.013 0.001 PHE A 652 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (11857) covalent geometry : angle 0.53866 / 0.27 (16275) hydrogen bonds : bond 0.03950 / 2.04 ( 593) hydrogen bonds : angle 3.99239 / 1.62 ( 1691) metal coordination : bond 0.00772 / 0.39 ( 7) metal coordination : angle 1.71052 / 0.57 ( 3) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.433 Fit side-chains REVERT: A 153 ASP cc_start: 0.7848 (p0) cc_final: 0.7572 (p0) REVERT: A 360 ASN cc_start: 0.6650 (OUTLIER) cc_final: 0.6159 (p0) REVERT: A 436 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: A 633 MET cc_start: 0.8534 (tmm) cc_final: 0.7972 (ttp) REVERT: A 892 HIS cc_start: 0.7901 (t-90) cc_final: 0.7672 (t-90) REVERT: A 902 MET cc_start: 0.6303 (mtp) cc_final: 0.5656 (ptm) REVERT: A 924 MET cc_start: 0.9028 (mmm) cc_final: 0.8730 (mmt) REVERT: B 55 MET cc_start: 0.2596 (mmt) cc_final: 0.2344 (mtm) REVERT: B 95 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6731 (pp) REVERT: B 104 ASN cc_start: 0.8053 (m-40) cc_final: 0.7849 (m110) REVERT: B 171 GLU cc_start: 0.7761 (tt0) cc_final: 0.7448 (tt0) REVERT: B 174 MET cc_start: 0.8145 (tpt) cc_final: 0.7943 (tpp) REVERT: C 23 GLU cc_start: 0.8853 (pt0) cc_final: 0.8616 (pt0) REVERT: G 55 MET cc_start: 0.7338 (mtp) cc_final: 0.6344 (pp-130) REVERT: G 99 ASP cc_start: 0.7287 (t0) cc_final: 0.6862 (t0) REVERT: G 136 ASN cc_start: 0.6373 (p0) cc_final: 0.6135 (p0) REVERT: G 161 ASP cc_start: 0.6519 (t0) cc_final: 0.6168 (t0) outliers start: 30 outliers final: 16 residues processed: 161 average time/residue: 0.4846 time to fit residues: 86.2093 Evaluate side-chains 151 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 103 optimal weight: 0.0370 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 403 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 158 GLN B 179 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099777 restraints weight = 15987.277| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.00 r_work: 0.3061 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11865 Z= 0.172 Angle : 0.572 8.170 16278 Z= 0.285 Chirality : 0.045 0.241 1862 Planarity : 0.004 0.050 1915 Dihedral : 8.196 56.351 1980 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.00 % Allowed : 15.27 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1313 helix: 0.82 (0.21), residues: 663 sheet: -0.70 (0.39), residues: 151 loop : -0.31 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.020 0.002 TYR A 87 PHE 0.014 0.002 PHE A 741 TRP 0.011 0.001 TRP A 290 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (11857) covalent geometry : angle 0.57100 / 0.28 (16275) hydrogen bonds : bond 0.04433 / 2.29 ( 593) hydrogen bonds : angle 4.02724 / 1.63 ( 1691) metal coordination : bond 0.01188 / 0.59 ( 7) metal coordination : angle 1.87275 / 0.62 ( 3) Misc. bond : bond 0.00118 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.439 Fit side-chains REVERT: A 153 ASP cc_start: 0.7872 (p0) cc_final: 0.7596 (p0) REVERT: A 436 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: A 633 MET cc_start: 0.8595 (tmm) cc_final: 0.8069 (ttp) REVERT: A 758 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8518 (tp) REVERT: A 892 HIS cc_start: 0.7872 (t-90) cc_final: 0.7664 (t-90) REVERT: A 902 MET cc_start: 0.6294 (mtp) cc_final: 0.5648 (ptm) REVERT: A 924 MET cc_start: 0.9107 (mmm) cc_final: 0.8775 (mmt) REVERT: B 38 LEU cc_start: 0.0428 (OUTLIER) cc_final: 0.0212 (pp) REVERT: B 55 MET cc_start: 0.2463 (mmt) cc_final: 0.2217 (mtm) REVERT: B 95 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6668 (pp) REVERT: B 171 GLU cc_start: 0.7780 (tt0) cc_final: 0.7462 (tt0) REVERT: B 174 MET cc_start: 0.8166 (tpt) cc_final: 0.7934 (tpp) REVERT: G 55 MET cc_start: 0.7338 (mtp) cc_final: 0.6349 (pp-130) REVERT: G 99 ASP cc_start: 0.7365 (t0) cc_final: 0.6955 (t0) REVERT: G 136 ASN cc_start: 0.6399 (p0) cc_final: 0.6129 (p0) outliers start: 35 outliers final: 21 residues processed: 158 average time/residue: 0.4900 time to fit residues: 85.6178 Evaluate side-chains 149 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 132 optimal weight: 0.0670 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** 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 = 0.3854 r_free = 0.3854 target = 0.143226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103350 restraints weight = 15984.135| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.87 r_work: 0.3118 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11865 Z= 0.103 Angle : 0.525 7.775 16278 Z= 0.261 Chirality : 0.043 0.256 1862 Planarity : 0.003 0.051 1915 Dihedral : 8.107 56.802 1980 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.66 % Allowed : 16.30 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1313 helix: 0.96 (0.21), residues: 663 sheet: -0.46 (0.40), residues: 143 loop : -0.23 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.019 0.001 TYR A 87 PHE 0.012 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (11857) covalent geometry : angle 0.52493 / 0.26 (16275) hydrogen bonds : bond 0.03700 / 1.91 ( 593) hydrogen bonds : angle 3.88456 / 1.58 ( 1691) metal coordination : bond 0.00666 / 0.33 ( 7) metal coordination : angle 1.62700 / 0.54 ( 3) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.447 Fit side-chains REVERT: A 57 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.5834 (tm-30) REVERT: A 153 ASP cc_start: 0.7781 (p0) cc_final: 0.7484 (p0) REVERT: A 223 ILE cc_start: 0.8837 (pt) cc_final: 0.8576 (mt) REVERT: A 372 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8029 (mp) REVERT: A 436 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: A 633 MET cc_start: 0.8543 (tmm) cc_final: 0.7960 (ttp) REVERT: A 757 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9122 (mm) REVERT: A 758 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 902 MET cc_start: 0.6223 (mtp) cc_final: 0.5716 (ptm) REVERT: A 924 MET cc_start: 0.8962 (mmm) cc_final: 0.8674 (mmt) REVERT: B 55 MET cc_start: 0.2295 (mmt) cc_final: 0.2092 (mtm) REVERT: B 95 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6721 (pp) REVERT: B 100 ASN cc_start: 0.6984 (p0) cc_final: 0.6566 (p0) REVERT: B 174 MET cc_start: 0.8039 (tpt) cc_final: 0.7822 (tpp) REVERT: G 55 MET cc_start: 0.7359 (mtp) cc_final: 0.6385 (pp-130) REVERT: G 75 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7287 (mmm-85) REVERT: G 99 ASP cc_start: 0.7343 (t0) cc_final: 0.6943 (t0) outliers start: 31 outliers final: 18 residues processed: 159 average time/residue: 0.5226 time to fit residues: 91.3156 Evaluate side-chains 158 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 35 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 0.0570 chunk 8 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 403 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 108 ASN B 136 ASN B 158 GLN B 179 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104875 restraints weight = 16115.160| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.87 r_work: 0.3147 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11865 Z= 0.094 Angle : 0.520 8.751 16278 Z= 0.257 Chirality : 0.042 0.245 1862 Planarity : 0.003 0.051 1915 Dihedral : 7.999 57.302 1980 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.32 % Allowed : 17.07 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1313 helix: 1.15 (0.21), residues: 663 sheet: -0.32 (0.42), residues: 133 loop : -0.19 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.017 0.001 TYR A 87 PHE 0.012 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.000 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (11857) covalent geometry : angle 0.51935 / 0.26 (16275) hydrogen bonds : bond 0.03409 / 1.76 ( 593) hydrogen bonds : angle 3.77392 / 1.53 ( 1691) metal coordination : bond 0.00516 / 0.26 ( 7) metal coordination : angle 1.30539 / 0.44 ( 3) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.434 Fit side-chains REVERT: A 57 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.5916 (tm-30) REVERT: A 77 PHE cc_start: 0.8245 (t80) cc_final: 0.8010 (t80) REVERT: A 153 ASP cc_start: 0.7744 (p0) cc_final: 0.7439 (p0) REVERT: A 633 MET cc_start: 0.8516 (tmm) cc_final: 0.7902 (ttp) REVERT: A 757 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9125 (mm) REVERT: A 758 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8636 (tp) REVERT: A 902 MET cc_start: 0.6142 (mtp) cc_final: 0.5636 (ptm) REVERT: A 924 MET cc_start: 0.8921 (mmm) cc_final: 0.8621 (mmt) REVERT: B 38 LEU cc_start: 0.0832 (OUTLIER) cc_final: 0.0628 (pp) REVERT: B 55 MET cc_start: 0.2361 (mmt) cc_final: 0.2157 (mtm) REVERT: B 95 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6636 (pp) REVERT: B 174 MET cc_start: 0.8074 (tpt) cc_final: 0.7862 (tpp) REVERT: G 55 MET cc_start: 0.7323 (mtp) cc_final: 0.6378 (pp-130) REVERT: G 75 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7292 (mmm-85) REVERT: G 94 MET cc_start: 0.8756 (mtp) cc_final: 0.8521 (ptp) REVERT: G 99 ASP cc_start: 0.7300 (t0) cc_final: 0.6908 (t0) outliers start: 27 outliers final: 13 residues processed: 164 average time/residue: 0.4925 time to fit residues: 89.1252 Evaluate side-chains 147 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** 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 = 0.3825 r_free = 0.3825 target = 0.140995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100059 restraints weight = 15837.203| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.94 r_work: 0.3076 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11865 Z= 0.178 Angle : 0.586 12.211 16278 Z= 0.290 Chirality : 0.045 0.211 1862 Planarity : 0.004 0.052 1915 Dihedral : 8.077 57.635 1980 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.14 % Allowed : 17.84 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1313 helix: 1.06 (0.20), residues: 665 sheet: -0.45 (0.40), residues: 143 loop : -0.25 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.019 0.002 TYR G 138 PHE 0.014 0.002 PHE A 741 TRP 0.010 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (11857) covalent geometry : angle 0.58548 / 0.29 (16275) hydrogen bonds : bond 0.04350 / 2.25 ( 593) hydrogen bonds : angle 3.95404 / 1.59 ( 1691) metal coordination : bond 0.01129 / 0.56 ( 7) metal coordination : angle 1.97112 / 0.66 ( 3) Misc. bond : bond 0.00129 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 57 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.5698 (tm-30) REVERT: A 77 PHE cc_start: 0.8235 (t80) cc_final: 0.8014 (t80) REVERT: A 153 ASP cc_start: 0.7785 (p0) cc_final: 0.7478 (p0) REVERT: A 372 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7912 (mp) REVERT: A 633 MET cc_start: 0.8613 (tmm) cc_final: 0.8046 (ttp) REVERT: A 757 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9144 (mm) REVERT: A 758 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8502 (tp) REVERT: A 924 MET cc_start: 0.9100 (mmm) cc_final: 0.8790 (mmt) REVERT: B 92 PHE cc_start: 0.8279 (m-10) cc_final: 0.8065 (m-10) REVERT: B 95 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6593 (pp) REVERT: B 174 MET cc_start: 0.8137 (tpt) cc_final: 0.7883 (tpp) REVERT: G 55 MET cc_start: 0.7278 (mtp) cc_final: 0.6296 (pp-130) REVERT: G 75 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7312 (mmm-85) REVERT: G 94 MET cc_start: 0.8758 (mtp) cc_final: 0.8485 (ptp) REVERT: G 99 ASP cc_start: 0.7417 (t0) cc_final: 0.7025 (t0) REVERT: G 174 MET cc_start: 0.6489 (tpt) cc_final: 0.6247 (mmm) outliers start: 25 outliers final: 15 residues processed: 150 average time/residue: 0.5325 time to fit residues: 87.4070 Evaluate side-chains 154 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.0070 chunk 97 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN B 136 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** 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 = 0.3855 r_free = 0.3855 target = 0.143364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103409 restraints weight = 16055.139| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.87 r_work: 0.3112 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11865 Z= 0.104 Angle : 0.550 12.254 16278 Z= 0.271 Chirality : 0.043 0.237 1862 Planarity : 0.003 0.051 1915 Dihedral : 8.029 57.833 1980 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.54 % Allowed : 18.78 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1313 helix: 1.15 (0.21), residues: 663 sheet: -0.32 (0.40), residues: 143 loop : -0.14 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 624 TYR 0.018 0.001 TYR A 87 PHE 0.012 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (11857) covalent geometry : angle 0.54974 / 0.27 (16275) hydrogen bonds : bond 0.03662 / 1.89 ( 593) hydrogen bonds : angle 3.84663 / 1.56 ( 1691) metal coordination : bond 0.00673 / 0.34 ( 7) metal coordination : angle 1.63227 / 0.54 ( 3) Misc. bond : bond 0.00019 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.438 Fit side-chains REVERT: A 57 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.5861 (tm-30) REVERT: A 153 ASP cc_start: 0.7774 (p0) cc_final: 0.7478 (p0) REVERT: A 633 MET cc_start: 0.8578 (tmm) cc_final: 0.7974 (ttp) REVERT: A 757 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9151 (mm) REVERT: A 758 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8516 (tp) REVERT: A 924 MET cc_start: 0.9017 (mmm) cc_final: 0.8720 (mmt) REVERT: B 95 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6590 (pp) REVERT: B 174 MET cc_start: 0.8062 (tpt) cc_final: 0.7820 (tpp) REVERT: G 55 MET cc_start: 0.7275 (mtp) cc_final: 0.6292 (pp-130) REVERT: G 75 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7416 (mmm-85) REVERT: G 94 MET cc_start: 0.8767 (mtp) cc_final: 0.8503 (ptp) REVERT: G 99 ASP cc_start: 0.7348 (t0) cc_final: 0.6972 (t0) outliers start: 18 outliers final: 14 residues processed: 145 average time/residue: 0.5112 time to fit residues: 81.4854 Evaluate side-chains 142 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** 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 = 0.3853 r_free = 0.3853 target = 0.143234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103171 restraints weight = 16133.010| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.64 r_work: 0.3136 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11865 Z= 0.112 Angle : 0.547 12.195 16278 Z= 0.269 Chirality : 0.043 0.228 1862 Planarity : 0.003 0.051 1915 Dihedral : 7.968 58.140 1980 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.72 % Allowed : 18.70 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1313 helix: 1.22 (0.21), residues: 663 sheet: -0.28 (0.41), residues: 138 loop : -0.13 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.021 0.001 TYR G 138 PHE 0.013 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (11857) covalent geometry : angle 0.54663 / 0.27 (16275) hydrogen bonds : bond 0.03711 / 1.92 ( 593) hydrogen bonds : angle 3.80171 / 1.54 ( 1691) metal coordination : bond 0.00730 / 0.36 ( 7) metal coordination : angle 1.64824 / 0.55 ( 3) Misc. bond : bond 0.00057 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4566.83 seconds wall clock time: 78 minutes 39.76 seconds (4719.76 seconds total)