Starting phenix.real_space_refine on Thu Jul 2 22:06:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dfg_30663/07_2026/7dfg_30663.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dfg_30663/07_2026/7dfg_30663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dfg_30663/07_2026/7dfg_30663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dfg_30663/07_2026/7dfg_30663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dfg_30663/07_2026/7dfg_30663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dfg_30663/07_2026/7dfg_30663.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dfg_30663/07_2026/7dfg_30663.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dfg_30663/07_2026/7dfg_30663.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 33 5.49 5 Mg 4 5.21 5 S 70 5.16 5 C 6383 2.51 5 N 1707 2.21 5 O 2023 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10223 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "T" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'RNA': 16} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 7327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7327 Classifications: {'peptide': 908} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 877} Chain breaks: 2 Chain: "B" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 111} 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: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Chain: "P" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'1RP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 24 Unusual residues: {' MG': 4, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3015 SG CYS A 301 52.303 65.210 44.160 1.00 27.60 S ATOM 3056 SG CYS A 306 52.362 64.611 40.300 1.00 26.32 S ATOM 3088 SG CYS A 310 55.984 64.395 42.479 1.00 25.33 S ATOM 4496 SG CYS A 487 33.869 59.947 52.053 1.00 32.69 S ATOM 5749 SG CYS A 645 33.137 59.771 47.959 1.00 36.88 S ATOM 5755 SG CYS A 646 36.211 62.001 49.701 1.00 34.30 S Time building chain proxies: 1.95, per 1000 atoms: 0.19 Number of scatterers: 10223 At special positions: 0 Unit cell: (112.245, 93.003, 130.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 33 15.00 Mg 4 11.99 F 1 9.00 O 2023 8.00 N 1707 7.00 C 6383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 313.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 3 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 50.2% alpha, 17.5% beta 10 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.731A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.555A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.660A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.708A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.088A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 3.629A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.670A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.591A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.352A 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 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.972A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.568A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.919A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.521A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.954A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.635A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 662 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 789 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.573A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 4.223A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR A 896 " --> pdb=" O HIS A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 4.025A pdb=" N TYR A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 77 through 98 removed outlier: 3.971A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 4.420A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.613A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (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: 3.556A 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 40 removed outlier: 3.999A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.624A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 99 removed outlier: 4.035A pdb=" N ASP G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 removed outlier: 3.520A pdb=" N ARG G 111 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.539A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (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: 6.962A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.798A 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: 6.495A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.749A 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: 6.495A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.416A 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: 6.381A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (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: 6.491A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR G 146 " --> pdb=" O ASP G 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 128 through 132 removed outlier: 6.491A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS G 165 " --> pdb=" O ASP G 161 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2071 1.32 - 1.45: 2662 1.45 - 1.57: 5593 1.57 - 1.69: 59 1.69 - 1.81: 105 Bond restraints: 10490 Sorted by residual: bond pdb=" OAH 1RP P1201 " pdb=" PAX 1RP P1201 " ideal model delta sigma weight residual 1.670 1.362 0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C5' 1RP P1201 " pdb=" O5' 1RP P1201 " ideal model delta sigma weight residual 1.458 1.600 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" O3' A P 19 " pdb=" P U P 20 " ideal model delta sigma weight residual 1.607 1.510 0.097 1.50e-02 4.44e+03 4.20e+01 bond pdb=" C2' U P 20 " pdb=" C1' U P 20 " ideal model delta sigma weight residual 1.529 1.435 0.094 1.50e-02 4.44e+03 3.89e+01 bond pdb=" C5' U P 20 " pdb=" C4' U P 20 " ideal model delta sigma weight residual 1.508 1.416 0.092 1.50e-02 4.44e+03 3.79e+01 ... (remaining 10485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 14065 2.77 - 5.54: 266 5.54 - 8.30: 27 8.30 - 11.07: 10 11.07 - 13.84: 2 Bond angle restraints: 14370 Sorted by residual: angle pdb=" C4' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 102.60 95.17 7.43 1.00e+00 1.00e+00 5.52e+01 angle pdb=" O3' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 113.70 124.05 -10.35 1.50e+00 4.44e-01 4.77e+01 angle pdb=" O5' U P 20 " pdb=" C5' U P 20 " pdb=" C4' U P 20 " ideal model delta sigma weight residual 111.50 101.26 10.24 1.50e+00 4.44e-01 4.66e+01 angle pdb=" C3' A P 19 " pdb=" O3' A P 19 " pdb=" P U P 20 " ideal model delta sigma weight residual 120.20 130.35 -10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" C3' U P 20 " pdb=" C2' U P 20 " pdb=" O2' U P 20 " ideal model delta sigma weight residual 110.70 119.47 -8.77 1.50e+00 4.44e-01 3.42e+01 ... (remaining 14365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.68: 5983 27.68 - 55.35: 212 55.35 - 83.02: 13 83.02 - 110.70: 5 110.70 - 138.37: 5 Dihedral angle restraints: 6218 sinusoidal: 2658 harmonic: 3560 Sorted by residual: dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual 180.00 -139.61 -40.39 0 5.00e+00 4.00e-02 6.52e+01 dihedral pdb=" O4 POP A1003 " pdb=" O POP A1003 " pdb=" P2 POP A1003 " pdb=" P1 POP A1003 " ideal model delta sinusoidal sigma weight residual -57.41 80.96 -138.37 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" CA TRP G 182 " pdb=" C TRP G 182 " pdb=" N PRO G 183 " pdb=" CA PRO G 183 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 6215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1471 0.097 - 0.193: 165 0.193 - 0.290: 6 0.290 - 0.386: 2 0.386 - 0.482: 1 Chirality restraints: 1645 Sorted by residual: chirality pdb=" C4' U P 20 " pdb=" C5' U P 20 " pdb=" O4' U P 20 " pdb=" C3' U P 20 " both_signs ideal model delta sigma weight residual False -2.50 -2.01 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" C3' U P 20 " pdb=" C4' U P 20 " pdb=" O3' U P 20 " pdb=" C2' U P 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C2' U P 20 " pdb=" C3' U P 20 " pdb=" O2' U P 20 " pdb=" C1' U P 20 " both_signs ideal model delta sigma weight residual False -2.75 -2.44 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1642 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 242 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO A 243 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 927 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 115 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO B 116 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 116 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 116 " -0.030 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 125 2.63 - 3.20: 8468 3.20 - 3.76: 16587 3.76 - 4.33: 23883 4.33 - 4.90: 37826 Nonbonded interactions: 86889 Sorted by model distance: nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1007 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASP A 218 " pdb="MG MG A1008 " model vdw 2.090 2.170 nonbonded pdb=" O6 POP A1006 " pdb="MG MG A1007 " model vdw 2.099 2.170 nonbonded pdb=" O2 POP A1006 " pdb="MG MG A1007 " model vdw 2.150 2.170 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.259 3.040 ... (remaining 86884 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' and (resid 84 through 179 or resid 182 through 191)) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.012 0.308 10498 Z= 0.532 Angle : 0.984 13.842 14373 Z= 0.540 Chirality : 0.062 0.482 1645 Planarity : 0.007 0.060 1728 Dihedral : 14.690 138.374 3914 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.38 % Allowed : 5.64 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.19), residues: 1186 helix: -2.39 (0.16), residues: 541 sheet: -1.27 (0.38), residues: 150 loop : -1.56 (0.23), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 181 TYR 0.020 0.003 TYR A 867 PHE 0.032 0.004 PHE A 741 TRP 0.018 0.004 TRP G 154 HIS 0.019 0.002 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.01148 / 0.51 (10490) covalent geometry : angle 0.97931 / 0.54 (14370) hydrogen bonds : bond 0.17087 / 10.31 ( 481) hydrogen bonds : angle 6.39972 / 4.05 ( 1343) metal coordination : bond 0.14414 / 8.31 ( 7) metal coordination : angle 7.00163 / 2.33 ( 3) Misc. bond : bond 0.13028 / 6.51 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.368 Fit side-chains REVERT: A 224 GLN cc_start: 0.8415 (tt0) cc_final: 0.8193 (tt0) REVERT: A 424 VAL cc_start: 0.8858 (m) cc_final: 0.8657 (t) REVERT: A 761 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8187 (m-30) REVERT: B 176 ASN cc_start: 0.8083 (t0) cc_final: 0.7600 (t0) REVERT: C 27 LYS cc_start: 0.8518 (ttpt) cc_final: 0.8296 (ttmt) REVERT: C 51 LYS cc_start: 0.8376 (mttp) cc_final: 0.8167 (mttm) outliers start: 4 outliers final: 3 residues processed: 167 average time/residue: 0.5628 time to fit residues: 101.2009 Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN A 39 ASN A 57 GLN A 75 HIS A 113 HIS A 117 GLN A 191 GLN A 256 HIS A 439 HIS A 543 ASN A 691 ASN A 713 ASN A 773 GLN A 790 ASN B 105 ASN B 108 ASN B 179 ASN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096384 restraints weight = 12602.301| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.85 r_work: 0.3005 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10498 Z= 0.110 Angle : 0.502 6.900 14373 Z= 0.274 Chirality : 0.040 0.162 1645 Planarity : 0.004 0.040 1728 Dihedral : 10.341 129.056 1690 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.60 % Allowed : 10.71 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.22), residues: 1186 helix: -0.43 (0.21), residues: 537 sheet: -1.08 (0.38), residues: 155 loop : -0.77 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 889 TYR 0.017 0.001 TYR A 788 PHE 0.016 0.001 PHE A 652 TRP 0.016 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10490) covalent geometry : angle 0.50176 / 0.27 (14370) hydrogen bonds : bond 0.03851 / 2.24 ( 481) hydrogen bonds : angle 4.43479 / 2.83 ( 1343) metal coordination : bond 0.00343 / 0.22 ( 7) metal coordination : angle 1.65342 / 0.55 ( 3) Misc. bond : bond 0.00128 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8385 (tt) REVERT: A 138 ASN cc_start: 0.8099 (t0) cc_final: 0.7756 (t0) REVERT: B 176 ASN cc_start: 0.7950 (t0) cc_final: 0.7459 (t0) REVERT: G 90 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7863 (ptp) REVERT: G 101 ASP cc_start: 0.7447 (p0) cc_final: 0.7225 (p0) REVERT: G 117 LEU cc_start: 0.5982 (mm) cc_final: 0.5695 (mm) outliers start: 17 outliers final: 6 residues processed: 171 average time/residue: 0.5164 time to fit residues: 95.4849 Evaluate side-chains 152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 90 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 75 HIS A 468 GLN A 572 HIS ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 HIS A 790 ASN A 791 ASN A 886 GLN B 158 GLN C 19 GLN C 36 HIS C 37 ASN G 105 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.091317 restraints weight = 12621.249| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.84 r_work: 0.2918 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 10498 Z= 0.324 Angle : 0.626 7.542 14373 Z= 0.334 Chirality : 0.048 0.173 1645 Planarity : 0.004 0.041 1728 Dihedral : 10.324 120.591 1686 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.20 % Allowed : 12.78 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1186 helix: -0.10 (0.21), residues: 547 sheet: -1.07 (0.37), residues: 156 loop : -0.69 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 889 TYR 0.019 0.002 TYR A 149 PHE 0.025 0.003 PHE A 741 TRP 0.013 0.002 TRP G 154 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.32 (10490) covalent geometry : angle 0.62490 / 0.33 (14370) hydrogen bonds : bond 0.05395 / 3.20 ( 481) hydrogen bonds : angle 4.59983 / 2.93 ( 1343) metal coordination : bond 0.01172 / 0.60 ( 7) metal coordination : angle 2.02965 / 0.68 ( 3) Misc. bond : bond 0.00223 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 105 ARG cc_start: 0.7633 (mmm160) cc_final: 0.7343 (mmm160) REVERT: A 138 ASN cc_start: 0.8236 (t0) cc_final: 0.7823 (t0) REVERT: A 340 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.5892 (t80) REVERT: A 889 ARG cc_start: 0.8173 (tpt-90) cc_final: 0.7847 (tpt-90) REVERT: A 922 GLU cc_start: 0.8671 (tt0) cc_final: 0.8116 (tp30) REVERT: A 924 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8346 (mmm) REVERT: B 176 ASN cc_start: 0.8034 (t0) cc_final: 0.7491 (t0) outliers start: 34 outliers final: 15 residues processed: 163 average time/residue: 0.4840 time to fit residues: 85.3694 Evaluate side-chains 159 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 118 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A 886 GLN C 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096874 restraints weight = 12657.535| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.96 r_work: 0.2980 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10498 Z= 0.103 Angle : 0.472 6.632 14373 Z= 0.257 Chirality : 0.041 0.166 1645 Planarity : 0.003 0.033 1728 Dihedral : 9.150 112.725 1686 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.26 % Allowed : 14.10 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1186 helix: 0.47 (0.22), residues: 551 sheet: -0.79 (0.39), residues: 141 loop : -0.39 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 889 TYR 0.013 0.001 TYR A 788 PHE 0.014 0.001 PHE A 652 TRP 0.016 0.001 TRP A 916 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (10490) covalent geometry : angle 0.47183 / 0.26 (14370) hydrogen bonds : bond 0.03422 / 1.99 ( 481) hydrogen bonds : angle 4.08001 / 2.59 ( 1343) metal coordination : bond 0.00238 / 0.13 ( 7) metal coordination : angle 1.49420 / 0.50 ( 3) Misc. bond : bond 0.00120 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 92 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7577 (p0) REVERT: A 105 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7311 (tpt90) REVERT: A 138 ASN cc_start: 0.8211 (t0) cc_final: 0.7817 (t0) REVERT: A 277 GLU cc_start: 0.8010 (pm20) cc_final: 0.7803 (pm20) REVERT: A 340 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.5526 (t80) REVERT: A 394 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8450 (t) REVERT: A 695 ASN cc_start: 0.9069 (t0) cc_final: 0.8819 (t160) REVERT: A 889 ARG cc_start: 0.8166 (tpt-90) cc_final: 0.7866 (tpt-90) REVERT: A 922 GLU cc_start: 0.8577 (tt0) cc_final: 0.8054 (tp30) REVERT: B 176 ASN cc_start: 0.7982 (t0) cc_final: 0.7402 (t0) REVERT: C 3 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7331 (tpp) outliers start: 24 outliers final: 7 residues processed: 162 average time/residue: 0.4565 time to fit residues: 80.1610 Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 790 ASN A 886 GLN A 892 HIS B 179 ASN C 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094872 restraints weight = 12592.209| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.85 r_work: 0.2981 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10498 Z= 0.134 Angle : 0.488 6.265 14373 Z= 0.262 Chirality : 0.041 0.166 1645 Planarity : 0.003 0.031 1728 Dihedral : 8.871 112.352 1686 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.44 % Allowed : 14.57 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.24), residues: 1186 helix: 0.61 (0.22), residues: 555 sheet: -0.75 (0.38), residues: 150 loop : -0.28 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.014 0.001 TYR A 788 PHE 0.016 0.001 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (10490) covalent geometry : angle 0.48740 / 0.26 (14370) hydrogen bonds : bond 0.03764 / 2.21 ( 481) hydrogen bonds : angle 4.04420 / 2.56 ( 1343) metal coordination : bond 0.00266 / 0.15 ( 7) metal coordination : angle 1.37381 / 0.46 ( 3) Misc. bond : bond 0.00127 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8370 (tt) REVERT: A 92 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7528 (p0) REVERT: A 105 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7284 (tpt170) REVERT: A 138 ASN cc_start: 0.8270 (t0) cc_final: 0.7832 (t0) REVERT: A 226 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 340 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.5598 (t80) REVERT: A 394 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8475 (t) REVERT: A 431 GLU cc_start: 0.7611 (mp0) cc_final: 0.7062 (mm-30) REVERT: A 889 ARG cc_start: 0.8192 (tpt-90) cc_final: 0.7880 (tpt-90) REVERT: A 922 GLU cc_start: 0.8541 (tt0) cc_final: 0.8092 (tp30) REVERT: B 176 ASN cc_start: 0.7984 (t0) cc_final: 0.7366 (t0) REVERT: C 3 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7365 (tpp) outliers start: 26 outliers final: 11 residues processed: 158 average time/residue: 0.4862 time to fit residues: 83.0897 Evaluate side-chains 162 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 114 optimal weight: 9.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 790 ASN A 886 GLN A 892 HIS C 19 GLN C 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.135859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095957 restraints weight = 12783.203| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.91 r_work: 0.2965 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10498 Z= 0.139 Angle : 0.485 6.263 14373 Z= 0.261 Chirality : 0.042 0.163 1645 Planarity : 0.003 0.031 1728 Dihedral : 8.665 113.085 1686 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.73 % Allowed : 14.47 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.24), residues: 1186 helix: 0.71 (0.22), residues: 555 sheet: -0.62 (0.39), residues: 146 loop : -0.26 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.014 0.001 TYR A 788 PHE 0.016 0.001 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10490) covalent geometry : angle 0.48454 / 0.26 (14370) hydrogen bonds : bond 0.03724 / 2.18 ( 481) hydrogen bonds : angle 4.01390 / 2.55 ( 1343) metal coordination : bond 0.00296 / 0.17 ( 7) metal coordination : angle 1.36497 / 0.45 ( 3) Misc. bond : bond 0.00139 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8333 (tt) REVERT: A 105 ARG cc_start: 0.7721 (mmm160) cc_final: 0.7279 (tpt170) REVERT: A 138 ASN cc_start: 0.8189 (t0) cc_final: 0.7846 (t0) REVERT: A 226 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8166 (p) REVERT: A 340 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.5580 (t80) REVERT: A 394 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8451 (t) REVERT: A 889 ARG cc_start: 0.8186 (tpt-90) cc_final: 0.7860 (tpt-90) REVERT: A 922 GLU cc_start: 0.8624 (tt0) cc_final: 0.8144 (tp30) REVERT: A 924 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8398 (mmm) REVERT: B 176 ASN cc_start: 0.7981 (t0) cc_final: 0.7419 (t0) REVERT: C 3 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7349 (tpp) outliers start: 29 outliers final: 13 residues processed: 163 average time/residue: 0.4893 time to fit residues: 86.5589 Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 0.0060 chunk 112 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 886 GLN A 892 HIS C 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.096323 restraints weight = 12675.114| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.02 r_work: 0.2983 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10498 Z= 0.139 Angle : 0.491 6.316 14373 Z= 0.264 Chirality : 0.041 0.160 1645 Planarity : 0.003 0.030 1728 Dihedral : 8.649 113.120 1686 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.44 % Allowed : 15.79 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1186 helix: 0.78 (0.23), residues: 557 sheet: -0.57 (0.39), residues: 146 loop : -0.23 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.014 0.001 TYR A 788 PHE 0.016 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10490) covalent geometry : angle 0.49108 / 0.26 (14370) hydrogen bonds : bond 0.03731 / 2.19 ( 481) hydrogen bonds : angle 3.99032 / 2.53 ( 1343) metal coordination : bond 0.00314 / 0.18 ( 7) metal coordination : angle 1.38807 / 0.46 ( 3) Misc. bond : bond 0.00142 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8333 (tt) REVERT: A 138 ASN cc_start: 0.8171 (t0) cc_final: 0.7884 (t0) REVERT: A 333 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 340 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.5614 (t80) REVERT: A 394 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8446 (t) REVERT: A 430 LYS cc_start: 0.7586 (mttm) cc_final: 0.7283 (mmtm) REVERT: A 889 ARG cc_start: 0.8184 (tpt-90) cc_final: 0.7861 (tpt-90) REVERT: A 922 GLU cc_start: 0.8618 (tt0) cc_final: 0.8089 (tp30) REVERT: B 176 ASN cc_start: 0.7971 (t0) cc_final: 0.7419 (t0) REVERT: C 3 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7375 (tpp) REVERT: G 90 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7825 (ptp) outliers start: 26 outliers final: 14 residues processed: 156 average time/residue: 0.4757 time to fit residues: 80.5033 Evaluate side-chains 163 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 91 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 886 GLN A 892 HIS C 19 GLN C 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098397 restraints weight = 12664.947| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.97 r_work: 0.3015 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10498 Z= 0.109 Angle : 0.467 6.175 14373 Z= 0.250 Chirality : 0.040 0.160 1645 Planarity : 0.003 0.029 1728 Dihedral : 8.211 111.849 1684 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.88 % Allowed : 16.82 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1186 helix: 0.94 (0.23), residues: 556 sheet: -0.40 (0.41), residues: 134 loop : -0.17 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.013 0.001 TYR A 788 PHE 0.014 0.001 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10490) covalent geometry : angle 0.46626 / 0.25 (14370) hydrogen bonds : bond 0.03370 / 1.97 ( 481) hydrogen bonds : angle 3.89375 / 2.46 ( 1343) metal coordination : bond 0.00289 / 0.16 ( 7) metal coordination : angle 1.29825 / 0.43 ( 3) Misc. bond : bond 0.00136 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8357 (tt) REVERT: A 105 ARG cc_start: 0.7640 (mmm160) cc_final: 0.7307 (tpt170) REVERT: A 138 ASN cc_start: 0.8028 (t0) cc_final: 0.7751 (t0) REVERT: A 340 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.5441 (t80) REVERT: A 394 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8453 (t) REVERT: A 889 ARG cc_start: 0.8180 (tpt-90) cc_final: 0.7873 (tpt-90) REVERT: A 922 GLU cc_start: 0.8561 (tt0) cc_final: 0.8094 (tp30) REVERT: B 176 ASN cc_start: 0.7981 (t0) cc_final: 0.7435 (t0) REVERT: C 3 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7302 (tpp) REVERT: G 90 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7786 (ptp) outliers start: 20 outliers final: 9 residues processed: 155 average time/residue: 0.4836 time to fit residues: 81.6084 Evaluate side-chains 156 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 90 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 886 GLN A 892 HIS C 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098073 restraints weight = 12657.876| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.86 r_work: 0.3013 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10498 Z= 0.107 Angle : 0.475 8.997 14373 Z= 0.252 Chirality : 0.040 0.158 1645 Planarity : 0.003 0.028 1728 Dihedral : 8.064 111.436 1684 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.79 % Allowed : 17.67 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1186 helix: 1.01 (0.23), residues: 556 sheet: -0.42 (0.41), residues: 134 loop : -0.11 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.012 0.001 TYR A 788 PHE 0.013 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10490) covalent geometry : angle 0.47481 / 0.25 (14370) hydrogen bonds : bond 0.03310 / 1.94 ( 481) hydrogen bonds : angle 3.85790 / 2.42 ( 1343) metal coordination : bond 0.00251 / 0.14 ( 7) metal coordination : angle 1.22208 / 0.41 ( 3) Misc. bond : bond 0.00137 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8341 (tt) REVERT: A 81 GLN cc_start: 0.8164 (tp40) cc_final: 0.7688 (mp10) REVERT: A 105 ARG cc_start: 0.7635 (mmm160) cc_final: 0.7218 (tpt170) REVERT: A 138 ASN cc_start: 0.8001 (t0) cc_final: 0.7732 (t0) REVERT: A 340 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.5386 (t80) REVERT: A 394 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8458 (t) REVERT: A 889 ARG cc_start: 0.8184 (tpt-90) cc_final: 0.7878 (tpt-90) REVERT: A 922 GLU cc_start: 0.8562 (tt0) cc_final: 0.8337 (tp30) REVERT: B 176 ASN cc_start: 0.7986 (t0) cc_final: 0.7423 (t0) REVERT: C 3 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7310 (tpp) outliers start: 19 outliers final: 12 residues processed: 152 average time/residue: 0.4951 time to fit residues: 81.7454 Evaluate side-chains 157 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 0.0570 chunk 110 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 886 GLN A 892 HIS C 19 GLN C 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097374 restraints weight = 12499.583| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.90 r_work: 0.2989 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10498 Z= 0.118 Angle : 0.486 9.488 14373 Z= 0.257 Chirality : 0.041 0.156 1645 Planarity : 0.003 0.032 1728 Dihedral : 8.081 111.910 1684 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.50 % Allowed : 18.33 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.24), residues: 1186 helix: 1.08 (0.23), residues: 549 sheet: -0.42 (0.40), residues: 146 loop : -0.10 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.013 0.001 TYR A 788 PHE 0.014 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10490) covalent geometry : angle 0.48546 / 0.26 (14370) hydrogen bonds : bond 0.03459 / 2.03 ( 481) hydrogen bonds : angle 3.83114 / 2.40 ( 1343) metal coordination : bond 0.00272 / 0.16 ( 7) metal coordination : angle 1.20737 / 0.40 ( 3) Misc. bond : bond 0.00140 / 0.07 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 77 PHE cc_start: 0.7851 (t80) cc_final: 0.7604 (t80) REVERT: A 81 GLN cc_start: 0.8194 (tp40) cc_final: 0.7627 (mp10) REVERT: A 105 ARG cc_start: 0.7554 (mmm160) cc_final: 0.7172 (tpt170) REVERT: A 138 ASN cc_start: 0.8024 (t0) cc_final: 0.7746 (t0) REVERT: A 340 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.5457 (t80) REVERT: A 394 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8442 (t) REVERT: A 430 LYS cc_start: 0.7634 (mttm) cc_final: 0.7381 (mmtm) REVERT: A 889 ARG cc_start: 0.8180 (tpt-90) cc_final: 0.7863 (tpt-90) REVERT: A 922 GLU cc_start: 0.8588 (tt0) cc_final: 0.8122 (tp30) REVERT: B 176 ASN cc_start: 0.7964 (t0) cc_final: 0.7394 (t0) REVERT: C 3 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7303 (tpp) outliers start: 16 outliers final: 11 residues processed: 149 average time/residue: 0.5014 time to fit residues: 81.0497 Evaluate side-chains 156 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 886 GLN A 892 HIS C 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098495 restraints weight = 12647.784| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.06 r_work: 0.3010 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10498 Z= 0.110 Angle : 0.479 9.226 14373 Z= 0.253 Chirality : 0.040 0.152 1645 Planarity : 0.003 0.035 1728 Dihedral : 8.016 111.507 1684 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.69 % Allowed : 18.05 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1186 helix: 1.10 (0.23), residues: 549 sheet: -0.31 (0.41), residues: 134 loop : -0.06 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 555 TYR 0.012 0.001 TYR A 788 PHE 0.014 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10490) covalent geometry : angle 0.47851 / 0.25 (14370) hydrogen bonds : bond 0.03358 / 1.97 ( 481) hydrogen bonds : angle 3.80196 / 2.39 ( 1343) metal coordination : bond 0.00252 / 0.14 ( 7) metal coordination : angle 1.22227 / 0.41 ( 3) Misc. bond : bond 0.00141 / 0.07 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3728.33 seconds wall clock time: 64 minutes 17.04 seconds (3857.04 seconds total)