Starting phenix.real_space_refine on Fri Jul 3 04:24:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfq_40448/07_2026/8sfq_40448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfq_40448/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfq_40448/07_2026/8sfq_40448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfq_40448/07_2026/8sfq_40448.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfq_40448/07_2026/8sfq_40448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfq_40448/07_2026/8sfq_40448.cif" } 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-dev-6108/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: 2.62, per 1000 atoms: 0.22 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: 1.10 Conformation dependent library (CDL) restraints added in 494.3 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: 1.55 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: 3.08 Time building geometry restraints manager: 1.46 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: 2.720 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: 0.020 Process input model: 14.190 Find NCS groups from input model: 0.060 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- 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= 0.324 Angle : 1.129 25.966 17296 Z= 0.638 Chirality : 0.068 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 0.00553 / 0.32 (12500) covalent geometry : angle 1.12858 / 0.64 (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 : 0.385 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: 0.9222 (p) REVERT: A 1155 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9187 (tp) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.1182 time to fit residues: 15.6829 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 : 0.431 ------------------------------------------------------------------------------- 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 A 883 ASN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.029596 restraints weight = 78350.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.030904 restraints weight = 38161.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.031766 restraints weight = 24661.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.032339 restraints weight = 18573.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.032686 restraints weight = 15399.133| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12500 Z= 0.246 Angle : 0.677 12.317 17296 Z= 0.369 Chirality : 0.045 0.300 1930 Planarity : 0.005 0.058 1895 Dihedral : 19.735 170.654 2529 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.44 % Allowed : 16.61 % Favored : 80.96 % 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: 1.17 (0.24), residues: 1234 helix: 1.32 (0.21), residues: 615 sheet: -0.23 (0.44), residues: 144 loop : 0.60 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 392 TYR 0.014 0.002 TYR A1236 PHE 0.019 0.001 PHE A 353 TRP 0.008 0.001 TRP A1258 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.25 (12500) covalent geometry : angle 0.67712 / 0.37 (17296) hydrogen bonds : bond 0.05070 / 3.36 ( 610) hydrogen bonds : angle 4.85478 / 3.47 ( 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 89 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9758 (mtpt) cc_final: 0.9436 (ptpp) REVERT: A 555 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8646 (tp) REVERT: A 593 MET cc_start: 0.9183 (tmm) cc_final: 0.8878 (tmm) REVERT: A 908 ASP cc_start: 0.7945 (t0) cc_final: 0.7490 (t0) REVERT: A 1012 TYR cc_start: 0.8442 (m-80) cc_final: 0.8044 (m-80) REVERT: A 1215 MET cc_start: 0.9313 (ptm) cc_final: 0.9075 (ptp) outliers start: 27 outliers final: 13 residues processed: 85 average time/residue: 0.1009 time to fit residues: 13.2415 Evaluate side-chains 66 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 555 ILE 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: 8.9990 chunk 37 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS A 620 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.039998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.029167 restraints weight = 79103.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.030425 restraints weight = 38853.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.031260 restraints weight = 25307.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.031765 restraints weight = 19155.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.032141 restraints weight = 16085.830| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12500 Z= 0.258 Angle : 0.655 13.944 17296 Z= 0.356 Chirality : 0.044 0.318 1930 Planarity : 0.004 0.042 1895 Dihedral : 19.653 175.611 2521 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.16 % Allowed : 16.34 % 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: 1.46 (0.24), residues: 1234 helix: 1.61 (0.21), residues: 614 sheet: -0.28 (0.44), residues: 144 loop : 0.72 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 912 TYR 0.018 0.002 TYR A 61 PHE 0.019 0.002 PHE A1249 TRP 0.011 0.001 TRP A1258 HIS 0.007 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.26 (12500) covalent geometry : angle 0.65546 / 0.36 (17296) hydrogen bonds : bond 0.04959 / 3.28 ( 610) hydrogen bonds : angle 4.58920 / 3.27 ( 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 91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9759 (mtpt) cc_final: 0.9421 (ptpp) REVERT: A 471 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9210 (tp) REVERT: A 908 ASP cc_start: 0.8017 (t0) cc_final: 0.7471 (t0) REVERT: A 1012 TYR cc_start: 0.8408 (m-80) cc_final: 0.8146 (m-80) REVERT: A 1099 GLU cc_start: 0.9532 (OUTLIER) cc_final: 0.9248 (pt0) REVERT: A 1133 MET cc_start: 0.9041 (mmp) cc_final: 0.8777 (mmp) outliers start: 35 outliers final: 17 residues processed: 86 average time/residue: 0.0931 time to fit residues: 12.5847 Evaluate side-chains 71 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 215 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 433 GLU 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: 0.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.040584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.029616 restraints weight = 77875.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030952 restraints weight = 37821.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.031824 restraints weight = 24300.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032380 restraints weight = 18217.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.032715 restraints weight = 15157.952| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12500 Z= 0.152 Angle : 0.581 13.416 17296 Z= 0.314 Chirality : 0.042 0.348 1930 Planarity : 0.003 0.038 1895 Dihedral : 19.665 179.631 2521 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.44 % Allowed : 17.24 % Favored : 80.32 % 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: 1.66 (0.25), residues: 1234 helix: 1.75 (0.21), residues: 617 sheet: -0.06 (0.46), residues: 134 loop : 0.78 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 912 TYR 0.015 0.001 TYR A 764 PHE 0.014 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (12500) covalent geometry : angle 0.58099 / 0.31 (17296) hydrogen bonds : bond 0.04160 / 2.76 ( 610) hydrogen bonds : angle 4.30601 / 3.07 ( 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 83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9755 (mtpt) cc_final: 0.9426 (ptpp) REVERT: A 471 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9194 (tp) REVERT: A 593 MET cc_start: 0.9274 (tmm) cc_final: 0.8949 (tmm) REVERT: A 908 ASP cc_start: 0.7825 (t0) cc_final: 0.7326 (t0) REVERT: A 965 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9293 (mmtm) REVERT: A 1133 MET cc_start: 0.9057 (mmp) cc_final: 0.8730 (mmp) outliers start: 27 outliers final: 15 residues processed: 78 average time/residue: 0.1005 time to fit residues: 12.2207 Evaluate side-chains 68 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN 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 471 LEU 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 786 GLU 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 965 LYS Chi-restraints excluded: chain A residue 1084 VAL 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: 6.9990 chunk 96 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 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 = 0.2948 r_free = 0.2948 target = 0.039272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028384 restraints weight = 80624.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.029638 restraints weight = 40009.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.030410 restraints weight = 26139.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.030952 restraints weight = 20139.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.031281 restraints weight = 16885.760| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12500 Z= 0.300 Angle : 0.655 13.704 17296 Z= 0.358 Chirality : 0.044 0.308 1930 Planarity : 0.004 0.036 1895 Dihedral : 19.652 179.755 2521 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.61 % Allowed : 16.79 % 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: 1.51 (0.24), residues: 1234 helix: 1.68 (0.21), residues: 618 sheet: -0.27 (0.44), residues: 146 loop : 0.70 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1094 TYR 0.021 0.002 TYR A1012 PHE 0.020 0.002 PHE A1249 TRP 0.011 0.001 TRP A1258 HIS 0.006 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.30 (12500) covalent geometry : angle 0.65473 / 0.36 (17296) hydrogen bonds : bond 0.05029 / 3.32 ( 610) hydrogen bonds : angle 4.49171 / 3.21 ( 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 88 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 48 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9761 (mtpt) cc_final: 0.9392 (mtmm) REVERT: A 908 ASP cc_start: 0.8128 (t0) cc_final: 0.7581 (t0) REVERT: A 965 LYS cc_start: 0.9575 (OUTLIER) cc_final: 0.9313 (mmtm) REVERT: A 1012 TYR cc_start: 0.8381 (m-80) cc_final: 0.8064 (m-80) REVERT: A 1055 MET cc_start: 0.8967 (tmm) cc_final: 0.8661 (tmm) REVERT: A 1099 GLU cc_start: 0.9503 (OUTLIER) cc_final: 0.9227 (pt0) REVERT: A 1133 MET cc_start: 0.9140 (mmp) cc_final: 0.8718 (mmp) outliers start: 40 outliers final: 25 residues processed: 80 average time/residue: 0.1081 time to fit residues: 13.1431 Evaluate side-chains 74 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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 345 VAL 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 786 GLU 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 959 SER Chi-restraints excluded: chain A residue 965 LYS 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 1099 GLU 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: 1.9990 chunk 1 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 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 = 0.2964 r_free = 0.2964 target = 0.040243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.029365 restraints weight = 78864.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.030652 restraints weight = 38902.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031488 restraints weight = 25309.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.031957 restraints weight = 19182.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.032367 restraints weight = 16298.367| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12500 Z= 0.204 Angle : 0.602 13.449 17296 Z= 0.328 Chirality : 0.043 0.333 1930 Planarity : 0.003 0.034 1895 Dihedral : 19.670 178.144 2521 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.89 % Allowed : 17.60 % 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: 1.67 (0.24), residues: 1234 helix: 1.78 (0.21), residues: 618 sheet: -0.12 (0.44), residues: 144 loop : 0.79 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 912 TYR 0.022 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 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (12500) covalent geometry : angle 0.60221 / 0.33 (17296) hydrogen bonds : bond 0.04368 / 2.90 ( 610) hydrogen bonds : angle 4.27687 / 3.05 ( 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 83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 51 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 MET cc_start: 0.9333 (tmm) cc_final: 0.8998 (tmm) REVERT: A 908 ASP cc_start: 0.8027 (t0) cc_final: 0.7514 (t0) REVERT: A 949 LYS cc_start: 0.9051 (ptpp) cc_final: 0.8834 (ptpp) REVERT: A 1012 TYR cc_start: 0.8362 (m-80) cc_final: 0.8012 (m-80) REVERT: A 1133 MET cc_start: 0.9115 (mmp) cc_final: 0.8675 (mmp) outliers start: 32 outliers final: 24 residues processed: 77 average time/residue: 0.1054 time to fit residues: 12.6650 Evaluate side-chains 74 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 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 1014 GLN Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain A residue 1225 MET 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: 0.0980 chunk 112 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 79 optimal weight: 0.0970 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN A1014 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.040694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.029853 restraints weight = 78462.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031163 restraints weight = 38201.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.031988 restraints weight = 24699.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032587 restraints weight = 18756.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.032946 restraints weight = 15467.865| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2134 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= 0.141 Angle : 0.577 10.855 17296 Z= 0.312 Chirality : 0.042 0.344 1930 Planarity : 0.003 0.034 1895 Dihedral : 19.641 176.313 2521 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.62 % Allowed : 18.05 % Favored : 79.33 % 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: 1.86 (0.25), residues: 1234 helix: 1.93 (0.21), residues: 610 sheet: 0.14 (0.46), residues: 134 loop : 0.83 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.022 0.001 TYR A1012 PHE 0.014 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 0.00284 / 0.14 (12500) covalent geometry : angle 0.57743 / 0.31 (17296) hydrogen bonds : bond 0.04077 / 2.71 ( 610) hydrogen bonds : angle 4.13676 / 2.95 ( 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: 29 poor density : 54 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9754 (mtpt) cc_final: 0.9446 (ptpp) REVERT: A 593 MET cc_start: 0.9293 (tmm) cc_final: 0.8968 (tmm) REVERT: A 908 ASP cc_start: 0.7927 (t0) cc_final: 0.7457 (t0) REVERT: A 1012 TYR cc_start: 0.8297 (m-80) cc_final: 0.7863 (m-80) REVERT: A 1046 THR cc_start: 0.9291 (p) cc_final: 0.9070 (p) REVERT: A 1055 MET cc_start: 0.8935 (tmm) cc_final: 0.8632 (tmm) REVERT: A 1133 MET cc_start: 0.9086 (mmp) cc_final: 0.8667 (mmp) outliers start: 29 outliers final: 24 residues processed: 75 average time/residue: 0.0958 time to fit residues: 11.1661 Evaluate side-chains 75 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 233 VAL 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 786 GLU 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 1013 GLN Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1223 LEU 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: 4.9990 chunk 118 optimal weight: 0.9980 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: 1.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 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 = 0.2960 r_free = 0.2960 target = 0.039472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.028649 restraints weight = 79819.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.029934 restraints weight = 38981.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.030791 restraints weight = 25227.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.031348 restraints weight = 18998.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.031699 restraints weight = 15805.893| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2284 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= 0.219 Angle : 0.601 12.829 17296 Z= 0.327 Chirality : 0.042 0.317 1930 Planarity : 0.003 0.034 1895 Dihedral : 19.610 176.555 2521 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.07 % Allowed : 17.69 % Favored : 79.24 % 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: 1.80 (0.25), residues: 1234 helix: 1.89 (0.21), residues: 618 sheet: -0.03 (0.44), residues: 142 loop : 0.84 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 411 TYR 0.020 0.002 TYR A1012 PHE 0.017 0.001 PHE A1249 TRP 0.011 0.001 TRP A1258 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (12500) covalent geometry : angle 0.60135 / 0.33 (17296) hydrogen bonds : bond 0.04417 / 2.92 ( 610) hydrogen bonds : angle 4.20900 / 2.99 ( 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 85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9759 (mtpt) cc_final: 0.9440 (mtmm) REVERT: A 908 ASP cc_start: 0.8073 (t0) cc_final: 0.7598 (t0) REVERT: A 1012 TYR cc_start: 0.8412 (m-80) cc_final: 0.7918 (m-80) REVERT: A 1055 MET cc_start: 0.9015 (tmm) cc_final: 0.8716 (tmm) REVERT: A 1133 MET cc_start: 0.9146 (mmp) cc_final: 0.8678 (mmp) outliers start: 34 outliers final: 26 residues processed: 75 average time/residue: 0.0844 time to fit residues: 9.9948 Evaluate side-chains 75 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 233 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 369 LYS 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 786 GLU 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 1013 GLN Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1210 HIS 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: 10.0000 chunk 124 optimal weight: 20.0000 chunk 122 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 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 = 0.2995 r_free = 0.2995 target = 0.041055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.030202 restraints weight = 77363.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.031515 restraints weight = 37986.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.032397 restraints weight = 24531.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.032957 restraints weight = 18367.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.033368 restraints weight = 15222.878| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12500 Z= 0.120 Angle : 0.594 12.063 17296 Z= 0.313 Chirality : 0.042 0.348 1930 Planarity : 0.003 0.034 1895 Dihedral : 19.576 174.329 2521 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.81 % Allowed : 19.04 % 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: 1.97 (0.25), residues: 1234 helix: 1.95 (0.21), residues: 616 sheet: 0.29 (0.47), residues: 132 loop : 0.94 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 386 TYR 0.022 0.001 TYR A1012 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 0.59421 / 0.31 (17296) hydrogen bonds : bond 0.03921 / 2.64 ( 610) hydrogen bonds : angle 4.00146 / 2.84 ( 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 75 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 MET cc_start: 0.9295 (tmm) cc_final: 0.9088 (tmm) REVERT: A 908 ASP cc_start: 0.7883 (t0) cc_final: 0.7430 (t0) REVERT: A 948 GLU cc_start: 0.9256 (tt0) cc_final: 0.8948 (tt0) REVERT: A 949 LYS cc_start: 0.8987 (ptpp) cc_final: 0.8775 (ptpp) REVERT: A 1012 TYR cc_start: 0.8374 (m-80) cc_final: 0.7845 (m-80) REVERT: A 1046 THR cc_start: 0.9294 (p) cc_final: 0.9085 (p) REVERT: A 1055 MET cc_start: 0.8990 (tmm) cc_final: 0.8667 (tmm) REVERT: A 1133 MET cc_start: 0.9096 (mmp) cc_final: 0.8663 (mmp) outliers start: 20 outliers final: 15 residues processed: 70 average time/residue: 0.0817 time to fit residues: 9.2316 Evaluate side-chains 70 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 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 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP 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 108 optimal weight: 7.9990 chunk 23 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 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 = 0.2998 r_free = 0.2998 target = 0.040776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.029877 restraints weight = 77869.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.031226 restraints weight = 37722.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032108 restraints weight = 24135.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.032659 restraints weight = 18125.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.033056 restraints weight = 15094.494| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12500 Z= 0.123 Angle : 0.577 11.270 17296 Z= 0.305 Chirality : 0.041 0.330 1930 Planarity : 0.003 0.034 1895 Dihedral : 19.467 173.657 2521 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.35 % Allowed : 19.68 % 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: 2.06 (0.25), residues: 1234 helix: 2.08 (0.21), residues: 610 sheet: 0.26 (0.47), residues: 132 loop : 0.95 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.020 0.001 TYR A1012 PHE 0.012 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 0.00246 / 0.12 (12500) covalent geometry : angle 0.57659 / 0.30 (17296) hydrogen bonds : bond 0.03835 / 2.59 ( 610) hydrogen bonds : angle 3.91949 / 2.78 ( 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 69 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 MET cc_start: 0.9292 (tmm) cc_final: 0.9087 (tmm) REVERT: A 908 ASP cc_start: 0.7900 (t0) cc_final: 0.7440 (t0) REVERT: A 948 GLU cc_start: 0.9265 (tt0) cc_final: 0.8958 (tt0) REVERT: A 1046 THR cc_start: 0.9318 (p) cc_final: 0.9117 (p) REVERT: A 1055 MET cc_start: 0.8991 (tmm) cc_final: 0.8659 (tmm) REVERT: A 1133 MET cc_start: 0.9114 (mmp) cc_final: 0.8677 (mmp) outliers start: 15 outliers final: 12 residues processed: 66 average time/residue: 0.0837 time to fit residues: 8.9975 Evaluate side-chains 64 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 315 THR 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 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: 10.0000 chunk 129 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 chunk 118 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 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 = 0.2983 r_free = 0.2983 target = 0.040338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.029455 restraints weight = 78430.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030768 restraints weight = 38091.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.031648 restraints weight = 24541.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.032229 restraints weight = 18414.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.032583 restraints weight = 15219.033| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12500 Z= 0.157 Angle : 0.589 11.485 17296 Z= 0.314 Chirality : 0.042 0.322 1930 Planarity : 0.003 0.033 1895 Dihedral : 19.442 173.867 2521 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.35 % Allowed : 19.40 % Favored : 79.24 % 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: 2.07 (0.25), residues: 1234 helix: 2.08 (0.21), residues: 612 sheet: 0.26 (0.47), residues: 132 loop : 0.96 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.013 0.001 TYR A 764 PHE 0.013 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (12500) covalent geometry : angle 0.58885 / 0.31 (17296) hydrogen bonds : bond 0.03959 / 2.66 ( 610) hydrogen bonds : angle 3.99596 / 2.85 ( 1667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.84 seconds wall clock time: 33 minutes 3.59 seconds (1983.59 seconds total)