Starting phenix.real_space_refine on Tue Jul 29 23:35:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dok_30795/07_2025/7dok_30795.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dok_30795/07_2025/7dok_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dok_30795/07_2025/7dok_30795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dok_30795/07_2025/7dok_30795.map" model { file = "/net/cci-nas-00/data/ceres_data/7dok_30795/07_2025/7dok_30795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dok_30795/07_2025/7dok_30795.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'RNA': 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: {'RNA': 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: 8.04, per 1000 atoms: 0.70 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: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.44 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: 6.44 Time building geometry restraints manager: 3.59 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: 16191 3.96 - 7.93: 67 7.93 - 11.89: 12 11.89 - 15.86: 2 15.86 - 19.82: 3 Bond angle restraints: 16275 Sorted by residual: angle pdb=" C4' U P 20 " pdb=" C3' U P 20 " pdb=" O3' U P 20 " ideal model delta sigma weight residual 113.00 123.86 -10.86 1.50e+00 4.44e-01 5.24e+01 angle pdb=" C2' G P 8 " pdb=" C1' G P 8 " pdb=" N9 G P 8 " ideal model delta sigma weight residual 112.00 101.41 10.59 1.50e+00 4.44e-01 4.98e+01 angle pdb=" O3' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 113.70 103.30 10.40 1.50e+00 4.44e-01 4.80e+01 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' U P 20 " pdb=" C1' U P 20 " pdb=" N1 U P 20 " ideal model delta sigma weight residual 112.00 102.26 9.74 1.50e+00 4.44e-01 4.22e+01 ... (remaining 16270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 6365 17.56 - 35.13: 625 35.13 - 52.69: 103 52.69 - 70.26: 49 70.26 - 87.82: 14 Dihedral angle restraints: 7156 sinusoidal: 3224 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 36.00 3.53 32.47 1 8.00e+00 1.56e-02 2.35e+01 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 25.00 -6.50 31.50 1 8.00e+00 1.56e-02 2.21e+01 dihedral pdb=" O4' G P 8 " pdb=" C2' G P 8 " pdb=" C1' G P 8 " pdb=" C3' G P 8 " ideal model delta sinusoidal sigma weight residual 25.00 -4.54 29.54 1 8.00e+00 1.56e-02 1.95e+01 ... (remaining 7153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 1861 0.287 - 0.573: 0 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 -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1' G P 8 " pdb=" O4' G P 8 " pdb=" C2' G P 8 " pdb=" N9 G P 8 " both_signs ideal model delta sigma weight residual False 2.46 2.72 -0.27 2.00e-01 2.50e+01 1.77e+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: 163.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 37.650 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 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:65.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 267.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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= 0.520 Angle : 1.022 19.823 16278 Z= 0.648 Chirality : 0.070 1.433 1862 Planarity : 0.006 0.065 1915 Dihedral : 14.740 87.824 4610 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 5.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (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 TRP 0.015 0.002 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.025 0.003 PHE C 49 TYR 0.022 0.002 TYR A 831 ARG 0.004 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.17792 ( 593) hydrogen bonds : angle 6.81290 ( 1691) metal coordination : bond 0.21484 ( 7) metal coordination : angle 8.00758 ( 3) covalent geometry : bond 0.00848 (11857) covalent geometry : angle 1.01653 (16275) Misc. bond : bond 0.05228 ( 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 : 2.332 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: 1.5024 time to fit residues: 336.6653 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 : 1.952 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 ASN A 75 HIS A 117 GLN 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 65 GLN 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 = 0.3836 r_free = 0.3836 target = 0.141940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101786 restraints weight = 15884.509| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.70 r_work: 0.3114 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11865 Z= 0.137 Angle : 0.534 6.530 16278 Z= 0.289 Chirality : 0.040 0.144 1862 Planarity : 0.004 0.051 1915 Dihedral : 11.791 79.343 2123 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.49 % Allowed : 10.38 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1313 helix: -0.05 (0.19), residues: 646 sheet: -0.62 (0.42), residues: 136 loop : -0.72 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 509 HIS 0.007 0.001 HIS C 36 PHE 0.015 0.002 PHE A 652 TYR 0.018 0.001 TYR A 87 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 593) hydrogen bonds : angle 4.50165 ( 1691) metal coordination : bond 0.01465 ( 7) metal coordination : angle 2.55512 ( 3) covalent geometry : bond 0.00296 (11857) covalent geometry : angle 0.53321 (16275) Misc. bond : bond 0.00015 ( 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 182 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7853 (p0) cc_final: 0.7647 (p0) REVERT: A 633 MET cc_start: 0.8502 (tmm) cc_final: 0.8043 (ttp) REVERT: A 714 LYS cc_start: 0.8483 (mmmm) cc_final: 0.7803 (mtpt) REVERT: A 755 MET cc_start: 0.9456 (mtm) cc_final: 0.9197 (mtm) REVERT: A 902 MET cc_start: 0.6454 (mtp) cc_final: 0.6208 (mtt) REVERT: A 924 MET cc_start: 0.9044 (mmm) cc_final: 0.8719 (mmt) REVERT: B 95 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6686 (pp) REVERT: C 23 GLU cc_start: 0.8926 (pt0) cc_final: 0.8699 (pt0) REVERT: G 55 MET cc_start: 0.7425 (mtp) cc_final: 0.6281 (pp-130) REVERT: G 59 LEU cc_start: 0.8154 (mt) cc_final: 0.7817 (mp) REVERT: G 99 ASP cc_start: 0.7245 (t0) cc_final: 0.6833 (OUTLIER) REVERT: G 136 ASN cc_start: 0.6596 (p0) cc_final: 0.6153 (p0) REVERT: G 174 MET cc_start: 0.6528 (tpt) cc_final: 0.6285 (mmm) outliers start: 29 outliers final: 14 residues processed: 170 average time/residue: 1.4948 time to fit residues: 279.5532 Evaluate side-chains 152 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL 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 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 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 1 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN A 642 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098064 restraints weight = 16037.138| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.75 r_work: 0.3051 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11865 Z= 0.266 Angle : 0.617 10.064 16278 Z= 0.326 Chirality : 0.045 0.166 1862 Planarity : 0.004 0.041 1915 Dihedral : 11.967 83.821 2120 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.77 % Allowed : 12.09 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1313 helix: 0.22 (0.20), residues: 657 sheet: -0.83 (0.40), residues: 151 loop : -0.70 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 290 HIS 0.008 0.001 HIS C 36 PHE 0.017 0.002 PHE A 652 TYR 0.017 0.002 TYR A 831 ARG 0.004 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.05526 ( 593) hydrogen bonds : angle 4.43688 ( 1691) metal coordination : bond 0.01821 ( 7) metal coordination : angle 2.65130 ( 3) covalent geometry : bond 0.00621 (11857) covalent geometry : angle 0.61578 (16275) Misc. bond : bond 0.00183 ( 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 175 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 2.391 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7876 (p0) cc_final: 0.7617 (p0) REVERT: A 159 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7132 (ttpp) REVERT: A 436 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: A 633 MET cc_start: 0.8596 (tmm) cc_final: 0.8109 (ttp) REVERT: A 666 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8814 (mtt) REVERT: A 892 HIS cc_start: 0.7896 (t-90) cc_final: 0.7683 (t-90) REVERT: A 902 MET cc_start: 0.6327 (mtp) cc_final: 0.5916 (ptm) REVERT: A 924 MET cc_start: 0.9137 (mmm) cc_final: 0.8742 (mmt) REVERT: B 95 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6711 (pp) REVERT: G 55 MET cc_start: 0.7410 (mtp) cc_final: 0.6355 (pp-130) REVERT: G 99 ASP cc_start: 0.7408 (t0) cc_final: 0.7001 (OUTLIER) REVERT: G 136 ASN cc_start: 0.6487 (p0) cc_final: 0.6282 (p0) outliers start: 44 outliers final: 22 residues processed: 158 average time/residue: 1.5510 time to fit residues: 267.2801 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 : 1.302 ------------------------------------------------------------------------------- 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 159 LYS Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 436 GLU 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 818 MET 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 907 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 94 MET 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 47 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN A 541 GLN A 543 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 = 0.3851 r_free = 0.3851 target = 0.143155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103306 restraints weight = 15901.921| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.88 r_work: 0.3115 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11865 Z= 0.101 Angle : 0.482 8.781 16278 Z= 0.256 Chirality : 0.039 0.135 1862 Planarity : 0.003 0.046 1915 Dihedral : 11.602 80.562 2120 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.57 % Allowed : 14.32 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1313 helix: 0.71 (0.21), residues: 660 sheet: -0.51 (0.40), residues: 143 loop : -0.40 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.013 0.001 PHE A 652 TYR 0.016 0.001 TYR A 87 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 593) hydrogen bonds : angle 3.99628 ( 1691) metal coordination : bond 0.00521 ( 7) metal coordination : angle 1.46063 ( 3) covalent geometry : bond 0.00211 (11857) covalent geometry : angle 0.48206 (16275) Misc. bond : bond 0.00029 ( 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 175 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.394 Fit side-chains REVERT: A 153 ASP cc_start: 0.7840 (p0) cc_final: 0.7566 (p0) REVERT: A 223 ILE cc_start: 0.8799 (pt) cc_final: 0.8529 (mt) REVERT: A 436 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: A 633 MET cc_start: 0.8517 (tmm) cc_final: 0.7956 (ttp) REVERT: A 892 HIS cc_start: 0.7853 (t-90) cc_final: 0.7594 (t-90) REVERT: A 902 MET cc_start: 0.6366 (mtp) cc_final: 0.5744 (ptm) REVERT: A 924 MET cc_start: 0.9024 (mmm) cc_final: 0.8707 (mmt) REVERT: B 38 LEU cc_start: 0.0315 (OUTLIER) cc_final: 0.0102 (pp) REVERT: B 55 MET cc_start: 0.2976 (mmt) cc_final: 0.2625 (mtm) REVERT: B 95 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6720 (pp) REVERT: G 55 MET cc_start: 0.7389 (mtp) cc_final: 0.6248 (pp-130) REVERT: G 59 LEU cc_start: 0.7907 (mt) cc_final: 0.7458 (mp) REVERT: G 75 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.7143 (mmm-85) REVERT: G 99 ASP cc_start: 0.7305 (t0) cc_final: 0.6908 (t0) REVERT: G 122 LEU cc_start: 0.7726 (mp) cc_final: 0.7375 (mp) REVERT: G 136 ASN cc_start: 0.6417 (p0) cc_final: 0.6164 (p0) outliers start: 30 outliers final: 11 residues processed: 167 average time/residue: 1.1510 time to fit residues: 210.2609 Evaluate side-chains 146 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 436 GLU 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 898 HIS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 38 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 chunk 126 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098477 restraints weight = 15810.562| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.76 r_work: 0.3063 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11865 Z= 0.227 Angle : 0.576 8.721 16278 Z= 0.302 Chirality : 0.044 0.167 1862 Planarity : 0.004 0.052 1915 Dihedral : 11.831 84.323 2120 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.17 % Allowed : 14.92 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1313 helix: 0.65 (0.20), residues: 658 sheet: -0.74 (0.40), residues: 151 loop : -0.48 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 290 HIS 0.007 0.001 HIS C 36 PHE 0.015 0.002 PHE A 652 TYR 0.019 0.002 TYR A 87 ARG 0.003 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 593) hydrogen bonds : angle 4.15196 ( 1691) metal coordination : bond 0.01513 ( 7) metal coordination : angle 2.29702 ( 3) covalent geometry : bond 0.00532 (11857) covalent geometry : angle 0.57488 (16275) Misc. bond : bond 0.00137 ( 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 164 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7867 (p0) cc_final: 0.7494 (p0) REVERT: A 436 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: A 633 MET cc_start: 0.8582 (tmm) cc_final: 0.8053 (ttp) REVERT: A 902 MET cc_start: 0.6231 (mtp) cc_final: 0.5738 (ptm) REVERT: A 924 MET cc_start: 0.9117 (mmm) cc_final: 0.8699 (mmt) REVERT: B 38 LEU cc_start: 0.0398 (OUTLIER) cc_final: 0.0190 (pp) REVERT: B 55 MET cc_start: 0.2486 (mmt) cc_final: 0.2258 (mtm) REVERT: B 95 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6733 (pp) REVERT: G 55 MET cc_start: 0.7380 (mtp) cc_final: 0.6376 (pp-130) REVERT: G 99 ASP cc_start: 0.7330 (t0) cc_final: 0.6918 (t0) REVERT: G 136 ASN cc_start: 0.6421 (p0) cc_final: 0.6193 (p0) outliers start: 37 outliers final: 25 residues processed: 151 average time/residue: 1.1720 time to fit residues: 193.7142 Evaluate side-chains 159 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 498 LEU Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 601 MET 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 854 LEU 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 907 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 LEU 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 59 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 18 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 88 GLN B 104 ASN B 136 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102907 restraints weight = 16014.290| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.73 r_work: 0.3132 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2191 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= 0.099 Angle : 0.483 7.913 16278 Z= 0.254 Chirality : 0.039 0.133 1862 Planarity : 0.003 0.050 1915 Dihedral : 11.598 81.110 2120 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.23 % Allowed : 16.12 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1313 helix: 0.89 (0.21), residues: 666 sheet: -0.47 (0.40), residues: 143 loop : -0.36 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.012 0.001 PHE A 652 TYR 0.017 0.001 TYR A 87 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 593) hydrogen bonds : angle 3.88440 ( 1691) metal coordination : bond 0.00606 ( 7) metal coordination : angle 1.48486 ( 3) covalent geometry : bond 0.00210 (11857) covalent geometry : angle 0.48312 (16275) Misc. bond : bond 0.00026 ( 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 164 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.178 Fit side-chains REVERT: A 57 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.5760 (tm-30) REVERT: A 153 ASP cc_start: 0.7818 (p0) cc_final: 0.7530 (p0) REVERT: A 223 ILE cc_start: 0.8839 (pt) cc_final: 0.8572 (mt) REVERT: A 633 MET cc_start: 0.8535 (tmm) cc_final: 0.7947 (ttp) REVERT: A 902 MET cc_start: 0.6289 (mtp) cc_final: 0.5740 (ptm) REVERT: A 924 MET cc_start: 0.9016 (mmm) cc_final: 0.8726 (mmt) REVERT: B 55 MET cc_start: 0.2435 (mmt) cc_final: 0.2234 (mtm) REVERT: B 95 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6627 (pp) REVERT: G 55 MET cc_start: 0.7372 (mtp) cc_final: 0.6391 (pp-130) REVERT: G 75 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7221 (mmm-85) REVERT: G 99 ASP cc_start: 0.7282 (t0) cc_final: 0.6879 (t0) REVERT: G 136 ASN cc_start: 0.6411 (p0) cc_final: 0.6089 (p0) outliers start: 26 outliers final: 12 residues processed: 156 average time/residue: 1.1082 time to fit residues: 189.2754 Evaluate side-chains 142 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 235 ASP 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 898 HIS Chi-restraints excluded: chain B residue 95 LEU 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 Chi-restraints excluded: chain G residue 160 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN A 892 HIS B 88 GLN B 136 ASN B 179 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098997 restraints weight = 16200.680| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.94 r_work: 0.3026 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11865 Z= 0.237 Angle : 0.585 8.697 16278 Z= 0.305 Chirality : 0.044 0.148 1862 Planarity : 0.004 0.050 1915 Dihedral : 11.832 84.843 2120 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.00 % Allowed : 15.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1313 helix: 0.75 (0.20), residues: 663 sheet: -0.74 (0.40), residues: 151 loop : -0.41 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 290 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.002 PHE G 147 TYR 0.021 0.002 TYR A 87 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 593) hydrogen bonds : angle 4.13369 ( 1691) metal coordination : bond 0.01536 ( 7) metal coordination : angle 2.29830 ( 3) covalent geometry : bond 0.00556 (11857) covalent geometry : angle 0.58388 (16275) Misc. bond : bond 0.00145 ( 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 164 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 57 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.5678 (tm-30) REVERT: A 153 ASP cc_start: 0.7845 (p0) cc_final: 0.7553 (p0) REVERT: A 633 MET cc_start: 0.8625 (tmm) cc_final: 0.8079 (ttp) REVERT: A 902 MET cc_start: 0.6271 (mtp) cc_final: 0.5753 (ptm) REVERT: A 924 MET cc_start: 0.9144 (mmm) cc_final: 0.8734 (mmt) REVERT: B 55 MET cc_start: 0.2468 (mmt) cc_final: 0.2262 (mtm) REVERT: B 95 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6731 (pp) REVERT: G 55 MET cc_start: 0.7344 (mtp) cc_final: 0.6410 (pp-130) REVERT: G 75 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.7447 (mmm-85) REVERT: G 99 ASP cc_start: 0.7375 (t0) cc_final: 0.6981 (t0) outliers start: 35 outliers final: 24 residues processed: 151 average time/residue: 1.1315 time to fit residues: 186.7508 Evaluate side-chains 151 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 235 ASP Chi-restraints excluded: chain A residue 333 ILE 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 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 896 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 42 LEU 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 59 LEU Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 160 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 90 optimal weight: 0.0670 chunk 119 optimal weight: 20.0000 chunk 133 optimal weight: 0.0000 chunk 105 optimal weight: 0.7980 overall best weight: 0.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 88 GLN B 104 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104366 restraints weight = 16185.418| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.86 r_work: 0.3127 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11865 Z= 0.097 Angle : 0.488 8.185 16278 Z= 0.256 Chirality : 0.038 0.139 1862 Planarity : 0.003 0.049 1915 Dihedral : 11.559 81.152 2120 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.23 % Allowed : 16.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1313 helix: 1.01 (0.21), residues: 662 sheet: -0.41 (0.41), residues: 143 loop : -0.26 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.012 0.001 PHE A 652 TYR 0.017 0.001 TYR A 87 ARG 0.004 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 593) hydrogen bonds : angle 3.85932 ( 1691) metal coordination : bond 0.00575 ( 7) metal coordination : angle 1.45863 ( 3) covalent geometry : bond 0.00196 (11857) covalent geometry : angle 0.48795 (16275) Misc. bond : bond 0.00022 ( 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 166 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.196 Fit side-chains REVERT: A 57 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.5842 (tm-30) REVERT: A 153 ASP cc_start: 0.7883 (p0) cc_final: 0.7594 (p0) REVERT: A 223 ILE cc_start: 0.8816 (pt) cc_final: 0.8555 (mt) REVERT: A 633 MET cc_start: 0.8512 (tmm) cc_final: 0.7915 (ttp) REVERT: A 924 MET cc_start: 0.8994 (mmm) cc_final: 0.8695 (mmt) REVERT: B 55 MET cc_start: 0.2193 (mmt) cc_final: 0.1983 (mtm) REVERT: B 95 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6897 (pp) REVERT: B 174 MET cc_start: 0.8180 (tpt) cc_final: 0.7856 (tpp) REVERT: G 55 MET cc_start: 0.7269 (mtp) cc_final: 0.6288 (pp-130) REVERT: G 75 ARG cc_start: 0.7608 (mmm-85) cc_final: 0.7236 (mmm-85) REVERT: G 99 ASP cc_start: 0.7338 (t0) cc_final: 0.6943 (t0) outliers start: 26 outliers final: 16 residues processed: 159 average time/residue: 1.0854 time to fit residues: 189.5086 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 : 1.251 ------------------------------------------------------------------------------- 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 136 GLU 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 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 42 LEU 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 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 114 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 0.0670 chunk 103 optimal weight: 0.0570 chunk 124 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 88 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102888 restraints weight = 16188.731| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.89 r_work: 0.3104 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11865 Z= 0.120 Angle : 0.509 12.305 16278 Z= 0.263 Chirality : 0.039 0.142 1862 Planarity : 0.003 0.049 1915 Dihedral : 11.563 80.853 2120 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.80 % Allowed : 17.67 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1313 helix: 1.10 (0.21), residues: 663 sheet: -0.37 (0.41), residues: 144 loop : -0.25 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.013 0.001 PHE A 741 TYR 0.020 0.001 TYR G 138 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 593) hydrogen bonds : angle 3.84558 ( 1691) metal coordination : bond 0.00846 ( 7) metal coordination : angle 1.74018 ( 3) covalent geometry : bond 0.00267 (11857) covalent geometry : angle 0.50813 (16275) Misc. bond : bond 0.00058 ( 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 151 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.198 Fit side-chains REVERT: A 57 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.5835 (tm-30) REVERT: A 77 PHE cc_start: 0.8277 (t80) cc_final: 0.8019 (t80) REVERT: A 153 ASP cc_start: 0.7872 (p0) cc_final: 0.7598 (p0) REVERT: A 633 MET cc_start: 0.8487 (tmm) cc_final: 0.7905 (ttp) REVERT: A 758 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8478 (tp) REVERT: A 924 MET cc_start: 0.8987 (mmm) cc_final: 0.8704 (mmt) REVERT: B 95 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6859 (pp) REVERT: B 174 MET cc_start: 0.8178 (tpt) cc_final: 0.7863 (tpp) REVERT: G 55 MET cc_start: 0.7312 (mtp) cc_final: 0.6346 (pp-130) REVERT: G 75 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7299 (mmm-85) REVERT: G 94 MET cc_start: 0.8763 (mtp) cc_final: 0.8555 (ptp) REVERT: G 99 ASP cc_start: 0.7369 (t0) cc_final: 0.7002 (t0) outliers start: 21 outliers final: 14 residues processed: 144 average time/residue: 1.7129 time to fit residues: 270.4335 Evaluate side-chains 151 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 601 MET 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 42 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 88 GLN B 136 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104108 restraints weight = 16077.781| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.88 r_work: 0.3124 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11865 Z= 0.105 Angle : 0.516 12.445 16278 Z= 0.264 Chirality : 0.039 0.170 1862 Planarity : 0.003 0.049 1915 Dihedral : 11.487 79.685 2120 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.72 % Allowed : 18.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1313 helix: 1.17 (0.21), residues: 663 sheet: -0.30 (0.41), residues: 144 loop : -0.16 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.012 0.001 PHE A 741 TYR 0.017 0.001 TYR A 87 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 593) hydrogen bonds : angle 3.82106 ( 1691) metal coordination : bond 0.00671 ( 7) metal coordination : angle 1.61197 ( 3) covalent geometry : bond 0.00228 (11857) covalent geometry : angle 0.51537 (16275) Misc. bond : bond 0.00037 ( 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 157 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.184 Fit side-chains REVERT: A 57 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.5863 (tm-30) REVERT: A 77 PHE cc_start: 0.8239 (t80) cc_final: 0.8027 (t80) REVERT: A 153 ASP cc_start: 0.7861 (p0) cc_final: 0.7578 (p0) REVERT: A 223 ILE cc_start: 0.8808 (pt) cc_final: 0.8560 (mt) REVERT: A 633 MET cc_start: 0.8451 (tmm) cc_final: 0.7868 (ttp) REVERT: A 758 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8437 (tp) REVERT: A 924 MET cc_start: 0.8964 (mmm) cc_final: 0.8695 (mmt) REVERT: B 95 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6815 (pp) REVERT: B 174 MET cc_start: 0.8141 (tpt) cc_final: 0.7827 (tpp) REVERT: G 55 MET cc_start: 0.7307 (mtp) cc_final: 0.6342 (pp-130) REVERT: G 75 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.7457 (mmm-85) REVERT: G 94 MET cc_start: 0.8770 (mtp) cc_final: 0.8545 (ptp) REVERT: G 99 ASP cc_start: 0.7463 (t0) cc_final: 0.7088 (t0) outliers start: 20 outliers final: 15 residues processed: 151 average time/residue: 1.0733 time to fit residues: 178.2077 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 : 1.286 ------------------------------------------------------------------------------- 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 601 MET 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 907 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 44 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 88 GLN B 136 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100250 restraints weight = 16026.544| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.68 r_work: 0.3084 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11865 Z= 0.203 Angle : 0.568 12.356 16278 Z= 0.293 Chirality : 0.043 0.143 1862 Planarity : 0.004 0.049 1915 Dihedral : 11.640 81.852 2120 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.97 % Allowed : 18.52 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1313 helix: 1.07 (0.21), residues: 665 sheet: -0.55 (0.40), residues: 150 loop : -0.27 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.002 PHE A 694 TYR 0.020 0.002 TYR A 87 ARG 0.003 0.000 ARG A 721 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 593) hydrogen bonds : angle 3.96056 ( 1691) metal coordination : bond 0.01299 ( 7) metal coordination : angle 1.99923 ( 3) covalent geometry : bond 0.00477 (11857) covalent geometry : angle 0.56768 (16275) Misc. bond : bond 0.00137 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10460.01 seconds wall clock time: 187 minutes 45.51 seconds (11265.51 seconds total)