Starting phenix.real_space_refine on Wed Aug 5 22:25:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfq_40448/08_2026/8sfq_40448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfq_40448/08_2026/8sfq_40448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sfq_40448/08_2026/8sfq_40448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfq_40448/08_2026/8sfq_40448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sfq_40448/08_2026/8sfq_40448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfq_40448/08_2026/8sfq_40448.map" } resolution = 3.5 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= -0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 91 5.49 5 S 23 5.16 5 C 7395 2.51 5 N 2050 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12045 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 10138 Classifications: {'peptide': 1240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1193} Chain breaks: 2 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 2.95, per 1000 atoms: 0.24 Number of scatterers: 12045 At special positions: 0 Unit cell: (89.964, 99.96, 137.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 91 15.00 O 2486 8.00 N 2050 7.00 C 7395 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=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 575.3 milliseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 55.9% alpha, 10.7% beta 40 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.660A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix removed outlier: 3.917A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.787A pdb=" N GLU A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 4.093A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 142 through 147 removed outlier: 4.094A pdb=" N LEU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 215 removed outlier: 4.050A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.625A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.837A pdb=" N PHE A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.521A pdb=" N SER A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 removed outlier: 3.502A pdb=" N ASN A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.567A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.934A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 429 through 452 Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.568A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 570 through 574 removed outlier: 4.167A pdb=" N GLY A 573 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.902A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.738A pdb=" N ASN A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.583A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.578A pdb=" N ILE A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.514A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 939 through 957 removed outlier: 3.663A pdb=" N LYS A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 3.662A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'A' and resid 1014 through 1025 removed outlier: 3.831A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.609A pdb=" N THR A1087 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A1088 " --> pdb=" O TRP A1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1088' Processing helix chain 'A' and resid 1090 through 1100 removed outlier: 3.639A pdb=" N GLY A1100 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1199 through 1205 removed outlier: 3.508A pdb=" N GLU A1205 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.620A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 removed outlier: 3.521A pdb=" N PHE A1253 " --> pdb=" O ASP A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1283 removed outlier: 3.626A pdb=" N GLU A1283 " --> pdb=" O ASN A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.651A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.301A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.651A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.852A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 931 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A 915 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ARG A 909 " --> pdb=" O GLU A 993 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1101 through 1107 removed outlier: 6.651A pdb=" N PHE A1101 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LYS A1118 " --> pdb=" O PHE A1101 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A1112 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA8, first strand: chain 'A' and resid 1159 through 1162 Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1229 523 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3172 1.34 - 1.46: 3308 1.46 - 1.58: 5799 1.58 - 1.70: 183 1.70 - 1.83: 38 Bond restraints: 12500 Sorted by residual: bond pdb=" C1' DT D 19 " pdb=" N1 DT D 19 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.25e+01 bond pdb=" C5' DA D 18 " pdb=" C4' DA D 18 " ideal model delta sigma weight residual 1.512 1.535 -0.023 7.00e-03 2.04e+04 1.08e+01 bond pdb=" C1' DC C 12 " pdb=" N1 DC C 12 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.11e+00 bond pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " ideal model delta sigma weight residual 1.435 1.399 0.036 1.30e-02 5.92e+03 7.77e+00 bond pdb=" C3' DA D 18 " pdb=" C2' DA D 18 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.66e+00 ... (remaining 12495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.19: 17165 5.19 - 10.39: 109 10.39 - 15.58: 18 15.58 - 20.77: 3 20.77 - 25.97: 1 Bond angle restraints: 17296 Sorted by residual: angle pdb=" CA PRO A 453 " pdb=" N PRO A 453 " pdb=" CD PRO A 453 " ideal model delta sigma weight residual 112.00 99.18 12.82 1.40e+00 5.10e-01 8.38e+01 angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 133.97 -25.97 3.00e+00 1.11e-01 7.49e+01 angle pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sigma weight residual 117.70 125.81 -8.11 1.20e+00 6.94e-01 4.57e+01 angle pdb=" N1 U B 12 " pdb=" C2 U B 12 " pdb=" O2 U B 12 " ideal model delta sigma weight residual 122.80 127.27 -4.47 7.00e-01 2.04e+00 4.08e+01 angle pdb=" O2 U B 12 " pdb=" C2 U B 12 " pdb=" N3 U B 12 " ideal model delta sigma weight residual 122.20 117.94 4.26 7.00e-01 2.04e+00 3.71e+01 ... (remaining 17291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.95: 6900 32.95 - 65.90: 497 65.90 - 98.85: 38 98.85 - 131.80: 0 131.80 - 164.75: 4 Dihedral angle restraints: 7439 sinusoidal: 3781 harmonic: 3658 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 51.52 148.48 1 1.50e+01 4.44e-03 7.90e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 68.02 131.98 1 1.50e+01 4.44e-03 7.12e+01 dihedral pdb=" CA ALA A1067 " pdb=" C ALA A1067 " pdb=" N PRO A1068 " pdb=" CA PRO A1068 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 7436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1878 0.151 - 0.303: 35 0.303 - 0.454: 14 0.454 - 0.606: 2 0.606 - 0.757: 1 Chirality restraints: 1930 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.34 -3.09 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" P DA C 28 " pdb=" OP1 DA C 28 " pdb=" OP2 DA C 28 " pdb=" O5' DA C 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" P DA C 8 " pdb=" OP1 DA C 8 " pdb=" OP2 DA C 8 " pdb=" O5' DA C 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.94e+00 ... (remaining 1927 not shown) Planarity restraints: 1895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 452 " 0.087 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO A 453 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 365 " -0.017 2.00e-02 2.50e+03 2.76e-02 1.34e+01 pdb=" CG PHE A 365 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 365 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 365 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 365 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 365 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 365 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1236 " 0.016 2.00e-02 2.50e+03 2.46e-02 1.22e+01 pdb=" CG TYR A1236 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A1236 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A1236 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A1236 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1236 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A1236 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1236 " -0.011 2.00e-02 2.50e+03 ... (remaining 1892 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1596 2.76 - 3.29: 11600 3.29 - 3.83: 22227 3.83 - 4.36: 25046 4.36 - 4.90: 40352 Nonbonded interactions: 100821 Sorted by model distance: nonbonded pdb=" NH1 ARG A 392 " pdb=" OG SER A 425 " model vdw 2.220 3.120 nonbonded pdb=" OG SER A 236 " pdb=" OE1 GLU A 238 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR A 88 " pdb=" OE1 GLU A 90 " model vdw 2.268 3.040 nonbonded pdb=" O LYS A 429 " pdb=" OG SER A 432 " model vdw 2.281 3.040 nonbonded pdb=" O HIS A1280 " pdb=" OG SER A1284 " model vdw 2.287 3.040 ... (remaining 100816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.980 Find NCS groups from input model: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.006 0.121 12500 Z= 0.327 Angle : 1.145 25.966 17296 Z= 0.657 Chirality : 0.070 0.757 1930 Planarity : 0.006 0.122 1895 Dihedral : 20.081 164.749 5071 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.72 % Allowed : 18.77 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.23), residues: 1234 helix: 0.23 (0.20), residues: 612 sheet: -0.01 (0.45), residues: 143 loop : 0.38 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 912 TYR 0.057 0.003 TYR A1236 PHE 0.058 0.003 PHE A 365 TRP 0.018 0.002 TRP A 483 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.33 (12500) covalent geometry : angle 1.14479 / 0.66 (17296) hydrogen bonds : bond 0.15025 / 9.78 ( 610) hydrogen bonds : angle 6.15449 / 4.39 ( 1667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1001 SER cc_start: 0.9511 (m) cc_final: 0.9214 (p) REVERT: A 1155 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9188 (tp) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.1041 time to fit residues: 13.8418 Evaluate side-chains 64 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1155 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 415 HIS ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 ASN A 946 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.040492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.029528 restraints weight = 78573.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.030830 restraints weight = 38298.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.031685 restraints weight = 24739.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.032243 restraints weight = 18667.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.032606 restraints weight = 15528.873| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12500 Z= 0.244 Angle : 0.684 12.365 17296 Z= 0.370 Chirality : 0.045 0.352 1930 Planarity : 0.005 0.060 1895 Dihedral : 19.699 174.488 2529 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.35 % Allowed : 16.79 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.24), residues: 1234 helix: 1.34 (0.21), residues: 615 sheet: -0.25 (0.44), residues: 144 loop : 0.62 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 912 TYR 0.015 0.002 TYR A1236 PHE 0.019 0.001 PHE A 353 TRP 0.009 0.001 TRP A1258 HIS 0.005 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.24 (12500) covalent geometry : angle 0.68358 / 0.37 (17296) hydrogen bonds : bond 0.05081 / 3.38 ( 610) hydrogen bonds : angle 4.82239 / 3.44 ( 1667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9758 (mtpt) cc_final: 0.9435 (ptpp) REVERT: A 593 MET cc_start: 0.9197 (tmm) cc_final: 0.8841 (tmm) REVERT: A 732 MET cc_start: 0.9635 (mmp) cc_final: 0.9420 (mmp) REVERT: A 908 ASP cc_start: 0.7895 (t0) cc_final: 0.7438 (t0) REVERT: A 1215 MET cc_start: 0.9340 (ptm) cc_final: 0.9100 (ptp) outliers start: 26 outliers final: 13 residues processed: 87 average time/residue: 0.0893 time to fit residues: 11.9946 Evaluate side-chains 66 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 916 TYR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 10 optimal weight: 7.9990 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 415 HIS A 620 GLN ** A 878 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 = 0.2983 r_free = 0.2983 target = 0.040547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.029575 restraints weight = 78273.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.030906 restraints weight = 37975.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.031763 restraints weight = 24467.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032330 restraints weight = 18430.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.032693 restraints weight = 15311.477| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12500 Z= 0.183 Angle : 0.610 12.994 17296 Z= 0.331 Chirality : 0.043 0.366 1930 Planarity : 0.004 0.039 1895 Dihedral : 19.589 178.894 2521 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.71 % Allowed : 16.43 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.25), residues: 1234 helix: 1.63 (0.21), residues: 616 sheet: -0.22 (0.45), residues: 144 loop : 0.79 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 912 TYR 0.020 0.002 TYR A1012 PHE 0.015 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (12500) covalent geometry : angle 0.61015 / 0.33 (17296) hydrogen bonds : bond 0.04476 / 2.97 ( 610) hydrogen bonds : angle 4.46338 / 3.18 ( 1667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9752 (mtpt) cc_final: 0.9417 (ptpp) REVERT: A 471 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9191 (tp) REVERT: A 908 ASP cc_start: 0.7869 (t0) cc_final: 0.7385 (t0) REVERT: A 949 LYS cc_start: 0.9162 (ptpp) cc_final: 0.8943 (ptpp) REVERT: A 1099 GLU cc_start: 0.9515 (OUTLIER) cc_final: 0.9231 (pt0) outliers start: 30 outliers final: 15 residues processed: 85 average time/residue: 0.0885 time to fit residues: 11.6333 Evaluate side-chains 72 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1013 GLN Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.029198 restraints weight = 79529.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.030491 restraints weight = 39383.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.031333 restraints weight = 25714.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.031856 restraints weight = 19484.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.032243 restraints weight = 16363.624| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12500 Z= 0.226 Angle : 0.617 13.212 17296 Z= 0.335 Chirality : 0.043 0.358 1930 Planarity : 0.003 0.036 1895 Dihedral : 19.557 178.765 2521 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.16 % Allowed : 16.43 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.25), residues: 1234 helix: 1.69 (0.21), residues: 618 sheet: -0.23 (0.44), residues: 144 loop : 0.79 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 951 TYR 0.016 0.002 TYR A 61 PHE 0.018 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.23 (12500) covalent geometry : angle 0.61708 / 0.33 (17296) hydrogen bonds : bond 0.04641 / 3.08 ( 610) hydrogen bonds : angle 4.39595 / 3.14 ( 1667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 51 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9757 (mtpt) cc_final: 0.9434 (ptpp) REVERT: A 593 MET cc_start: 0.9160 (tmm) cc_final: 0.8916 (tmm) REVERT: A 908 ASP cc_start: 0.7885 (t0) cc_final: 0.7362 (t0) REVERT: A 949 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8733 (pttp) REVERT: A 1012 TYR cc_start: 0.8428 (m-80) cc_final: 0.8077 (m-80) REVERT: A 1055 MET cc_start: 0.8904 (tmm) cc_final: 0.8592 (tmm) REVERT: A 1099 GLU cc_start: 0.9506 (OUTLIER) cc_final: 0.9217 (pt0) REVERT: A 1133 MET cc_start: 0.8874 (mmp) cc_final: 0.8639 (mmp) outliers start: 35 outliers final: 19 residues processed: 79 average time/residue: 0.0787 time to fit residues: 9.8175 Evaluate side-chains 69 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1013 GLN Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 30.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.040246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.029303 restraints weight = 79913.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.030602 restraints weight = 39432.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.031444 restraints weight = 25550.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.032010 restraints weight = 19373.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032354 restraints weight = 16093.567| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12500 Z= 0.182 Angle : 0.598 12.968 17296 Z= 0.321 Chirality : 0.042 0.365 1930 Planarity : 0.003 0.038 1895 Dihedral : 19.543 176.996 2521 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.89 % Allowed : 17.15 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.25), residues: 1234 helix: 1.81 (0.21), residues: 617 sheet: -0.09 (0.44), residues: 142 loop : 0.86 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.017 0.001 TYR A 61 PHE 0.015 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (12500) covalent geometry : angle 0.59769 / 0.32 (17296) hydrogen bonds : bond 0.04239 / 2.80 ( 610) hydrogen bonds : angle 4.27205 / 3.05 ( 1667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9759 (mtpt) cc_final: 0.9441 (ptpp) REVERT: A 537 MET cc_start: 0.9237 (mmt) cc_final: 0.8741 (mmt) REVERT: A 908 ASP cc_start: 0.7869 (t0) cc_final: 0.7368 (t0) REVERT: A 949 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8726 (pttp) REVERT: A 1012 TYR cc_start: 0.8361 (m-80) cc_final: 0.7970 (m-80) REVERT: A 1133 MET cc_start: 0.8998 (mmp) cc_final: 0.8686 (mmp) outliers start: 32 outliers final: 19 residues processed: 79 average time/residue: 0.0882 time to fit residues: 10.8551 Evaluate side-chains 68 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1013 GLN Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN A1014 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.039658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.028889 restraints weight = 80797.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.030145 restraints weight = 40465.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.030920 restraints weight = 26451.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.031485 restraints weight = 20320.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.031808 restraints weight = 16941.891| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 12500 Z= 0.300 Angle : 0.679 13.462 17296 Z= 0.365 Chirality : 0.044 0.337 1930 Planarity : 0.004 0.035 1895 Dihedral : 19.567 177.066 2521 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.25 % Allowed : 17.15 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.24), residues: 1234 helix: 1.70 (0.21), residues: 618 sheet: -0.17 (0.44), residues: 144 loop : 0.71 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 912 TYR 0.020 0.002 TYR A 61 PHE 0.020 0.002 PHE A1249 TRP 0.011 0.001 TRP A1258 HIS 0.007 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.30 (12500) covalent geometry : angle 0.67946 / 0.36 (17296) hydrogen bonds : bond 0.05035 / 3.33 ( 610) hydrogen bonds : angle 4.44030 / 3.16 ( 1667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 49 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9763 (mtpt) cc_final: 0.9396 (mtmm) REVERT: A 593 MET cc_start: 0.9207 (tmm) cc_final: 0.8943 (tmm) REVERT: A 908 ASP cc_start: 0.8160 (t0) cc_final: 0.7633 (t0) REVERT: A 949 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8706 (pttp) REVERT: A 1012 TYR cc_start: 0.8450 (m-80) cc_final: 0.8017 (m-80) REVERT: A 1055 MET cc_start: 0.8973 (tmm) cc_final: 0.8657 (tmm) REVERT: A 1133 MET cc_start: 0.9063 (mmp) cc_final: 0.8670 (mmp) outliers start: 36 outliers final: 29 residues processed: 78 average time/residue: 0.0839 time to fit residues: 10.4541 Evaluate side-chains 76 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 46 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1013 GLN Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 24 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 0.0470 chunk 55 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.029544 restraints weight = 78097.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030861 restraints weight = 38001.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.031769 restraints weight = 24510.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032302 restraints weight = 18313.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.032699 restraints weight = 15293.896| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12500 Z= 0.121 Angle : 0.591 12.863 17296 Z= 0.315 Chirality : 0.042 0.383 1930 Planarity : 0.003 0.033 1895 Dihedral : 19.541 173.642 2521 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 17.96 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.89 (0.25), residues: 1234 helix: 1.89 (0.21), residues: 617 sheet: 0.22 (0.46), residues: 133 loop : 0.90 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.015 0.001 TYR A 61 PHE 0.012 0.001 PHE A1249 TRP 0.012 0.001 TRP A1258 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (12500) covalent geometry : angle 0.59088 / 0.31 (17296) hydrogen bonds : bond 0.04030 / 2.69 ( 610) hydrogen bonds : angle 4.11905 / 2.94 ( 1667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9751 (mtpt) cc_final: 0.9442 (ptpp) REVERT: A 593 MET cc_start: 0.9148 (tmm) cc_final: 0.8901 (tmm) REVERT: A 908 ASP cc_start: 0.7851 (t0) cc_final: 0.7397 (t0) REVERT: A 949 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8719 (pttp) REVERT: A 1012 TYR cc_start: 0.8338 (m-80) cc_final: 0.7804 (m-80) REVERT: A 1046 THR cc_start: 0.9278 (p) cc_final: 0.9068 (p) REVERT: A 1055 MET cc_start: 0.8934 (tmm) cc_final: 0.8599 (tmm) REVERT: A 1133 MET cc_start: 0.9011 (mmp) cc_final: 0.8621 (mmp) outliers start: 28 outliers final: 17 residues processed: 75 average time/residue: 0.0784 time to fit residues: 9.3088 Evaluate side-chains 69 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 32 optimal weight: 0.0870 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.039410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.028619 restraints weight = 80161.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029888 restraints weight = 39551.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.030682 restraints weight = 25760.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.031247 restraints weight = 19742.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.031619 restraints weight = 16458.473| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12500 Z= 0.239 Angle : 0.630 12.655 17296 Z= 0.338 Chirality : 0.043 0.343 1930 Planarity : 0.003 0.034 1895 Dihedral : 19.503 174.725 2521 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.80 % Allowed : 18.05 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.25), residues: 1234 helix: 1.92 (0.21), residues: 618 sheet: -0.03 (0.45), residues: 143 loop : 0.84 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.018 0.002 TYR A 61 PHE 0.018 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.006 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.24 (12500) covalent geometry : angle 0.62995 / 0.34 (17296) hydrogen bonds : bond 0.04599 / 3.06 ( 610) hydrogen bonds : angle 4.26490 / 3.03 ( 1667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9762 (mtpt) cc_final: 0.9449 (mtmm) REVERT: A 908 ASP cc_start: 0.8085 (t0) cc_final: 0.7598 (t0) REVERT: A 949 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8757 (pttp) REVERT: A 1012 TYR cc_start: 0.8448 (m-80) cc_final: 0.7850 (m-80) REVERT: A 1133 MET cc_start: 0.9071 (mmp) cc_final: 0.8637 (mmp) outliers start: 31 outliers final: 22 residues processed: 72 average time/residue: 0.0830 time to fit residues: 9.6737 Evaluate side-chains 70 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.039776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.028971 restraints weight = 79536.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.030253 restraints weight = 39206.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.031089 restraints weight = 25564.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.031624 restraints weight = 19443.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.031962 restraints weight = 16239.229| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12500 Z= 0.177 Angle : 0.606 13.476 17296 Z= 0.324 Chirality : 0.042 0.357 1930 Planarity : 0.003 0.034 1895 Dihedral : 19.519 173.537 2521 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.26 % Allowed : 18.77 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.25), residues: 1234 helix: 1.94 (0.21), residues: 618 sheet: 0.08 (0.45), residues: 141 loop : 0.91 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.017 0.001 TYR A 61 PHE 0.016 0.001 PHE A1249 TRP 0.011 0.001 TRP A1258 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (12500) covalent geometry : angle 0.60592 / 0.32 (17296) hydrogen bonds : bond 0.04229 / 2.82 ( 610) hydrogen bonds : angle 4.18272 / 2.97 ( 1667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 908 ASP cc_start: 0.8054 (t0) cc_final: 0.7585 (t0) REVERT: A 949 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8753 (pttp) REVERT: A 1012 TYR cc_start: 0.8413 (m-80) cc_final: 0.7820 (m-80) REVERT: A 1133 MET cc_start: 0.9042 (mmp) cc_final: 0.8620 (mmp) outliers start: 25 outliers final: 19 residues processed: 68 average time/residue: 0.0850 time to fit residues: 9.2641 Evaluate side-chains 68 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 56 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.040457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.029527 restraints weight = 78362.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.030849 restraints weight = 38018.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.031700 restraints weight = 24436.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.032279 restraints weight = 18544.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.032648 restraints weight = 15303.333| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12500 Z= 0.130 Angle : 0.593 14.340 17296 Z= 0.313 Chirality : 0.042 0.369 1930 Planarity : 0.003 0.035 1895 Dihedral : 19.451 171.481 2521 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.81 % Allowed : 19.40 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.25), residues: 1234 helix: 2.02 (0.21), residues: 618 sheet: 0.28 (0.47), residues: 131 loop : 0.96 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.015 0.001 TYR A 595 PHE 0.013 0.001 PHE A1249 TRP 0.012 0.001 TRP A1258 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (12500) covalent geometry : angle 0.59270 / 0.31 (17296) hydrogen bonds : bond 0.03950 / 2.66 ( 610) hydrogen bonds : angle 4.03543 / 2.86 ( 1667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 908 ASP cc_start: 0.7961 (t0) cc_final: 0.7483 (t0) REVERT: A 949 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8750 (pttp) REVERT: A 1046 THR cc_start: 0.9315 (p) cc_final: 0.9111 (p) REVERT: A 1055 MET cc_start: 0.8951 (tmm) cc_final: 0.8654 (tmm) REVERT: A 1133 MET cc_start: 0.9030 (mmp) cc_final: 0.8628 (mmp) outliers start: 20 outliers final: 17 residues processed: 68 average time/residue: 0.0798 time to fit residues: 8.7558 Evaluate side-chains 70 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 6.9990 chunk 129 optimal weight: 10.9990 chunk 30 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 118 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.039957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.029069 restraints weight = 79587.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.030360 restraints weight = 38958.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.031232 restraints weight = 25213.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.031808 restraints weight = 18951.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.032147 restraints weight = 15699.062| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12500 Z= 0.180 Angle : 0.602 13.457 17296 Z= 0.321 Chirality : 0.042 0.347 1930 Planarity : 0.003 0.033 1895 Dihedral : 19.425 172.265 2521 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.81 % Allowed : 19.22 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.25), residues: 1234 helix: 2.03 (0.21), residues: 619 sheet: 0.01 (0.45), residues: 141 loop : 0.96 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 386 TYR 0.025 0.002 TYR A1012 PHE 0.016 0.001 PHE A1249 TRP 0.011 0.001 TRP A1258 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (12500) covalent geometry : angle 0.60182 / 0.32 (17296) hydrogen bonds : bond 0.04175 / 2.80 ( 610) hydrogen bonds : angle 4.08063 / 2.89 ( 1667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.60 seconds wall clock time: 29 minutes 58.50 seconds (1798.50 seconds total)