Starting phenix.real_space_refine on Fri Jul 3 09:36:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yn9_33955/07_2026/7yn9_33955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yn9_33955/07_2026/7yn9_33955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yn9_33955/07_2026/7yn9_33955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yn9_33955/07_2026/7yn9_33955.map" model { file = "/net/cci-nas-00/data/ceres_data/7yn9_33955/07_2026/7yn9_33955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yn9_33955/07_2026/7yn9_33955.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yn9_33955/07_2026/7yn9_33955.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yn9_33955/07_2026/7yn9_33955.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 38 5.49 5 S 56 5.16 5 C 8114 2.51 5 N 2329 2.21 5 O 2531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 13068 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1514, 12258 Classifications: {'peptide': 1514} Link IDs: {'PTRANS': 83, 'TRANS': 1430} Chain breaks: 4 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 17} Time building chain proxies: 2.68, per 1000 atoms: 0.21 Number of scatterers: 13068 At special positions: 0 Unit cell: (106.24, 171.81, 128.65, 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 56 16.00 P 38 15.00 O 2531 8.00 N 2329 7.00 C 8114 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: 1.06 Conformation dependent library (CDL) restraints added in 507.5 milliseconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 20 sheets defined 20.9% alpha, 15.9% beta 0 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.891A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 275 removed outlier: 3.610A pdb=" N ALA A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.745A pdb=" N ILE A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.693A pdb=" N ARG A 293 " --> pdb=" O ARG A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.534A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.437A pdb=" N GLU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 4.223A pdb=" N LEU A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 362' Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.797A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 555 removed outlier: 3.903A pdb=" N THR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 585 through 594 removed outlier: 3.990A pdb=" N ASN A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A 590 " --> pdb=" O ASN A 586 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.595A pdb=" N GLU A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.643A pdb=" N VAL A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.507A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.831A pdb=" N ILE A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 755 removed outlier: 4.148A pdb=" N LYS A 755 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 787 through 802 removed outlier: 3.515A pdb=" N ALA A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.654A pdb=" N ILE A 812 " --> pdb=" O LYS A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.882A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1232 through 1247 removed outlier: 3.859A pdb=" N LYS A1237 " --> pdb=" O LYS A1233 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A1238 " --> pdb=" O ALA A1234 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A1242 " --> pdb=" O TYR A1238 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A1243 " --> pdb=" O LYS A1239 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A1245 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.837A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1347 removed outlier: 3.517A pdb=" N ARG A1346 " --> pdb=" O CYS A1342 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A1347 " --> pdb=" O PRO A1343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1342 through 1347' Processing helix chain 'A' and resid 1420 through 1425 removed outlier: 3.550A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1476 removed outlier: 3.607A pdb=" N GLY A1469 " --> pdb=" O GLU A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1526 removed outlier: 3.904A pdb=" N GLY A1524 " --> pdb=" O PRO A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1534 removed outlier: 3.926A pdb=" N PHE A1534 " --> pdb=" O LEU A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1539 No H-bonds generated for 'chain 'A' and resid 1537 through 1539' Processing helix chain 'A' and resid 1540 through 1545 Processing helix chain 'A' and resid 1575 through 1579 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 5.876A pdb=" N GLU A 201 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A 153 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU A 203 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.573A pdb=" N GLY A 202 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 7 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 10 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.871A pdb=" N ARG A 171 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 485 removed outlier: 3.649A pdb=" N GLY A 408 " --> pdb=" O PHE A 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 3.649A pdb=" N GLY A 408 " --> pdb=" O PHE A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 498 removed outlier: 3.544A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 501 through 504 removed outlier: 9.986A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARG A 503 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 577 removed outlier: 3.702A pdb=" N TYR A 577 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 723 through 725 removed outlier: 3.728A pdb=" N VAL A 630 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 823 " --> pdb=" O ASN A 629 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 663 Processing sheet with id=AB2, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AB4, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.841A pdb=" N PHE A1456 " --> pdb=" O CYS A 897 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1227 through 1229 Processing sheet with id=AB6, first strand: chain 'A' and resid 1007 through 1012 removed outlier: 4.122A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1130 removed outlier: 3.727A pdb=" N TYR A1126 " --> pdb=" O ARG A1041 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A1041 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS A1128 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL A1039 " --> pdb=" O LYS A1128 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A1130 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N MET A1037 " --> pdb=" O PHE A1130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A1146 " --> pdb=" O VAL A1035 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1086 Processing sheet with id=AB9, first strand: chain 'A' and resid 1187 through 1188 removed outlier: 4.098A pdb=" N ASP A1187 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1200 through 1202 removed outlier: 3.672A pdb=" N CYS A1201 " --> pdb=" O TYR A1209 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1278 through 1280 removed outlier: 6.625A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3891 1.33 - 1.45: 2336 1.45 - 1.57: 7073 1.57 - 1.69: 75 1.69 - 1.81: 80 Bond restraints: 13455 Sorted by residual: bond pdb=" N CYS A 965 " pdb=" CA CYS A 965 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.22e-02 6.72e+03 6.57e+00 bond pdb=" N CYS A1312 " pdb=" CA CYS A1312 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.22e-02 6.72e+03 6.31e+00 bond pdb=" N CYS A 711 " pdb=" CA CYS A 711 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.35e-02 5.49e+03 5.61e+00 bond pdb=" N CYS A1345 " pdb=" CA CYS A1345 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.29e-02 6.01e+03 5.32e+00 bond pdb=" N CYS A 86 " pdb=" CA CYS A 86 " ideal model delta sigma weight residual 1.453 1.487 -0.035 1.51e-02 4.39e+03 5.25e+00 ... (remaining 13450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 17763 2.08 - 4.16: 485 4.16 - 6.24: 49 6.24 - 8.32: 10 8.32 - 10.40: 4 Bond angle restraints: 18311 Sorted by residual: angle pdb=" C ARG A 924 " pdb=" N LYS A 925 " pdb=" CA LYS A 925 " ideal model delta sigma weight residual 122.44 115.51 6.93 1.19e+00 7.06e-01 3.39e+01 angle pdb=" N CYS A1345 " pdb=" CA CYS A1345 " pdb=" C CYS A1345 " ideal model delta sigma weight residual 113.97 107.03 6.94 1.28e+00 6.10e-01 2.94e+01 angle pdb=" N VAL A 782 " pdb=" CA VAL A 782 " pdb=" C VAL A 782 " ideal model delta sigma weight residual 111.81 107.41 4.40 8.60e-01 1.35e+00 2.61e+01 angle pdb=" N ILE A 479 " pdb=" CA ILE A 479 " pdb=" C ILE A 479 " ideal model delta sigma weight residual 112.96 108.10 4.86 1.00e+00 1.00e+00 2.36e+01 angle pdb=" N VAL A1151 " pdb=" CA VAL A1151 " pdb=" C VAL A1151 " ideal model delta sigma weight residual 112.17 108.14 4.03 9.50e-01 1.11e+00 1.80e+01 ... (remaining 18306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 7888 35.49 - 70.97: 182 70.97 - 106.45: 15 106.45 - 141.94: 0 141.94 - 177.42: 1 Dihedral angle restraints: 8086 sinusoidal: 3719 harmonic: 4367 Sorted by residual: dihedral pdb=" CA TRP A1512 " pdb=" C TRP A1512 " pdb=" N ARG A1513 " pdb=" CA ARG A1513 " ideal model delta harmonic sigma weight residual 180.00 146.44 33.56 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" CA ALA A 425 " pdb=" C ALA A 425 " pdb=" N LYS A 426 " pdb=" CA LYS A 426 " ideal model delta harmonic sigma weight residual -180.00 -153.20 -26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA PHE A 990 " pdb=" C PHE A 990 " pdb=" N LEU A 991 " pdb=" CA LEU A 991 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 8083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1386 0.049 - 0.099: 448 0.099 - 0.148: 89 0.148 - 0.198: 10 0.198 - 0.247: 2 Chirality restraints: 1935 Sorted by residual: chirality pdb=" C3' U B -14 " pdb=" C4' U B -14 " pdb=" O3' U B -14 " pdb=" C2' U B -14 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA CYS A 123 " pdb=" N CYS A 123 " pdb=" C CYS A 123 " pdb=" CB CYS A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1' A B -2 " pdb=" O4' A B -2 " pdb=" C2' A B -2 " pdb=" N9 A B -2 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.19 2.00e-01 2.50e+01 9.07e-01 ... (remaining 1932 not shown) Planarity restraints: 2255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO A 864 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 768 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO A 769 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 765 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO A 766 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 766 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 766 " -0.038 5.00e-02 4.00e+02 ... (remaining 2252 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 643 2.70 - 3.25: 12390 3.25 - 3.80: 18833 3.80 - 4.35: 24617 4.35 - 4.90: 41635 Nonbonded interactions: 98118 Sorted by model distance: nonbonded pdb=" NE2 HIS A 865 " pdb=" OH TYR A1561 " model vdw 2.151 3.120 nonbonded pdb=" O SER A 211 " pdb=" NH1 ARG A 215 " model vdw 2.171 3.120 nonbonded pdb=" OH TYR A1014 " pdb=" OE2 GLU A1216 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASN A1088 " pdb=" OG1 THR A1092 " model vdw 2.212 3.040 nonbonded pdb=" NZ LYS A1004 " pdb=" O PHE A1005 " model vdw 2.218 3.120 ... (remaining 98113 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=1.00 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: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.160 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 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 : 0.007 0.062 13455 Z= 0.299 Angle : 0.830 10.399 18311 Z= 0.494 Chirality : 0.050 0.247 1935 Planarity : 0.006 0.105 2255 Dihedral : 15.336 177.424 5270 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 15.36 % Favored : 84.44 % Rotamer: Outliers : 0.38 % Allowed : 8.16 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -5.33 (0.16), residues: 1504 helix: -3.34 (0.23), residues: 274 sheet: -2.82 (0.30), residues: 250 loop : -4.07 (0.15), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.017 0.002 TYR A1245 PHE 0.023 0.002 PHE A 776 TRP 0.016 0.002 TRP A1466 HIS 0.005 0.001 HIS A1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.30 (13455) covalent geometry : angle 0.83015 / 0.49 (18311) hydrogen bonds : bond 0.28207 / 18.71 ( 232) hydrogen bonds : angle 8.89630 / 6.28 ( 675) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.490 Fit side-chains REVERT: A 86 CYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6771 (p) REVERT: A 315 TRP cc_start: 0.6436 (m100) cc_final: 0.6109 (m100) REVERT: A 711 CYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7830 (t) outliers start: 5 outliers final: 1 residues processed: 111 average time/residue: 0.1442 time to fit residues: 22.0006 Evaluate side-chains 74 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 1133 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 518 ASN A 531 GLN A 963 ASN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 HIS A1168 ASN A1247 ASN A1382 HIS A1417 HIS A1428 ASN A1452 ASN A1516 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.116603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.088082 restraints weight = 24567.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089064 restraints weight = 18166.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.089648 restraints weight = 14812.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090103 restraints weight = 11459.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.090199 restraints weight = 10678.505| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13455 Z= 0.167 Angle : 0.672 14.281 18311 Z= 0.351 Chirality : 0.046 0.228 1935 Planarity : 0.005 0.102 2255 Dihedral : 11.492 168.214 2115 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.57 % Favored : 87.23 % Rotamer: Outliers : 0.98 % Allowed : 13.29 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.48 (0.18), residues: 1504 helix: -2.23 (0.28), residues: 287 sheet: -2.30 (0.31), residues: 248 loop : -3.63 (0.16), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 621 TYR 0.012 0.001 TYR A1126 PHE 0.020 0.001 PHE A 776 TRP 0.020 0.001 TRP A1097 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (13455) covalent geometry : angle 0.67206 / 0.35 (18311) hydrogen bonds : bond 0.04584 / 2.96 ( 232) hydrogen bonds : angle 5.67415 / 4.02 ( 675) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.515 Fit side-chains REVERT: A 86 CYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7651 (p) REVERT: A 315 TRP cc_start: 0.6385 (m100) cc_final: 0.5968 (m100) REVERT: A 601 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8173 (mttm) REVERT: A 1211 MET cc_start: 0.8334 (tpt) cc_final: 0.7880 (tpt) outliers start: 13 outliers final: 6 residues processed: 93 average time/residue: 0.0931 time to fit residues: 13.3851 Evaluate side-chains 81 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 71 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 GLN ** A1056 GLN ** 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 = 0.3577 r_free = 0.3577 target = 0.116091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.087795 restraints weight = 24782.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.089407 restraints weight = 18007.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089757 restraints weight = 14411.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090095 restraints weight = 11050.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.090245 restraints weight = 10193.913| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13455 Z= 0.186 Angle : 0.655 12.575 18311 Z= 0.341 Chirality : 0.046 0.230 1935 Planarity : 0.005 0.101 2255 Dihedral : 11.342 167.713 2114 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.23 % Favored : 87.57 % Rotamer: Outliers : 1.66 % Allowed : 15.33 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.15 (0.19), residues: 1504 helix: -1.79 (0.29), residues: 295 sheet: -2.00 (0.31), residues: 255 loop : -3.52 (0.16), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.013 0.001 TYR A1126 PHE 0.021 0.002 PHE A 776 TRP 0.030 0.001 TRP A1097 HIS 0.003 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (13455) covalent geometry : angle 0.65453 / 0.34 (18311) hydrogen bonds : bond 0.04217 / 2.71 ( 232) hydrogen bonds : angle 5.17835 / 3.64 ( 675) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.322 Fit side-chains REVERT: A 315 TRP cc_start: 0.6430 (m100) cc_final: 0.6011 (m100) REVERT: A 1211 MET cc_start: 0.8501 (tpt) cc_final: 0.8063 (tpt) outliers start: 22 outliers final: 14 residues processed: 94 average time/residue: 0.1042 time to fit residues: 14.9926 Evaluate side-chains 85 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 148 optimal weight: 0.1980 chunk 43 optimal weight: 0.0030 chunk 127 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 931 HIS ** A1056 GLN ** 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 = 0.3646 r_free = 0.3646 target = 0.120821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092428 restraints weight = 24319.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093638 restraints weight = 17500.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.094372 restraints weight = 12633.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.094535 restraints weight = 10746.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094728 restraints weight = 10003.440| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13455 Z= 0.100 Angle : 0.579 14.094 18311 Z= 0.300 Chirality : 0.042 0.206 1935 Planarity : 0.005 0.086 2255 Dihedral : 11.045 166.141 2113 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.97 % Favored : 89.89 % Rotamer: Outliers : 1.59 % Allowed : 16.16 % Favored : 82.25 % 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: -3.73 (0.19), residues: 1504 helix: -1.25 (0.31), residues: 293 sheet: -1.84 (0.30), residues: 260 loop : -3.27 (0.17), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1036 TYR 0.008 0.001 TYR A 674 PHE 0.012 0.001 PHE A 776 TRP 0.036 0.001 TRP A1097 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (13455) covalent geometry : angle 0.57894 / 0.30 (18311) hydrogen bonds : bond 0.03003 / 1.92 ( 232) hydrogen bonds : angle 4.59608 / 3.22 ( 675) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.524 Fit side-chains REVERT: A 1082 TYR cc_start: 0.6789 (t80) cc_final: 0.6528 (t80) REVERT: A 1247 ASN cc_start: 0.8107 (m-40) cc_final: 0.7230 (p0) outliers start: 21 outliers final: 15 residues processed: 98 average time/residue: 0.1091 time to fit residues: 16.2500 Evaluate side-chains 89 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1056 GLN A1084 ASN A1095 HIS A1516 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088648 restraints weight = 24680.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.090095 restraints weight = 18148.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091015 restraints weight = 13035.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091099 restraints weight = 10125.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091143 restraints weight = 10270.209| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13455 Z= 0.182 Angle : 0.629 9.902 18311 Z= 0.325 Chirality : 0.045 0.225 1935 Planarity : 0.005 0.095 2255 Dihedral : 11.039 166.620 2113 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.64 % Favored : 88.16 % Rotamer: Outliers : 2.11 % Allowed : 16.62 % Favored : 81.27 % 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: -3.68 (0.19), residues: 1504 helix: -1.37 (0.30), residues: 310 sheet: -1.70 (0.31), residues: 266 loop : -3.25 (0.17), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.012 0.001 TYR A1126 PHE 0.020 0.001 PHE A 776 TRP 0.035 0.001 TRP A1097 HIS 0.004 0.001 HIS A 931 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (13455) covalent geometry : angle 0.62855 / 0.32 (18311) hydrogen bonds : bond 0.03573 / 2.28 ( 232) hydrogen bonds : angle 4.70737 / 3.30 ( 675) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.496 Fit side-chains REVERT: A 25 ARG cc_start: 0.7487 (mtm180) cc_final: 0.7283 (mtm180) REVERT: A 410 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7427 (pp) REVERT: A 1082 TYR cc_start: 0.6625 (t80) cc_final: 0.6339 (t80) REVERT: A 1211 MET cc_start: 0.8414 (tpt) cc_final: 0.7676 (tpt) REVERT: A 1530 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8633 (mp) outliers start: 28 outliers final: 20 residues processed: 100 average time/residue: 0.0956 time to fit residues: 15.3028 Evaluate side-chains 95 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 118 optimal weight: 0.0270 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 2.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1418 HIS A1516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.115560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087004 restraints weight = 24608.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.088094 restraints weight = 18049.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088558 restraints weight = 14765.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088948 restraints weight = 11550.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.089083 restraints weight = 10600.776| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13455 Z= 0.221 Angle : 0.673 12.563 18311 Z= 0.347 Chirality : 0.046 0.236 1935 Planarity : 0.005 0.095 2255 Dihedral : 11.187 167.465 2113 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.37 % Favored : 87.43 % Rotamer: Outliers : 2.11 % Allowed : 17.37 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.20), residues: 1504 helix: -1.24 (0.30), residues: 303 sheet: -1.78 (0.31), residues: 280 loop : -3.23 (0.17), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.013 0.001 TYR A1276 PHE 0.023 0.002 PHE A 776 TRP 0.040 0.002 TRP A1097 HIS 0.004 0.001 HIS A1095 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (13455) covalent geometry : angle 0.67252 / 0.35 (18311) hydrogen bonds : bond 0.03904 / 2.49 ( 232) hydrogen bonds : angle 4.86229 / 3.43 ( 675) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.510 Fit side-chains REVERT: A 410 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7543 (pp) REVERT: A 1211 MET cc_start: 0.8478 (tpt) cc_final: 0.7785 (tpt) REVERT: A 1530 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8664 (mp) outliers start: 28 outliers final: 23 residues processed: 93 average time/residue: 0.1064 time to fit residues: 15.2533 Evaluate side-chains 94 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1539 ASP Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1084 ASN A1516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091141 restraints weight = 24432.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092666 restraints weight = 17828.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093339 restraints weight = 13309.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093670 restraints weight = 10138.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093747 restraints weight = 9669.816| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13455 Z= 0.111 Angle : 0.586 13.759 18311 Z= 0.301 Chirality : 0.043 0.214 1935 Planarity : 0.005 0.089 2255 Dihedral : 10.996 166.579 2113 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.44 % Favored : 89.43 % Rotamer: Outliers : 1.89 % Allowed : 18.35 % Favored : 79.76 % 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: -3.35 (0.20), residues: 1504 helix: -0.91 (0.31), residues: 304 sheet: -1.45 (0.32), residues: 257 loop : -3.11 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 25 TYR 0.016 0.001 TYR A1082 PHE 0.014 0.001 PHE A 776 TRP 0.042 0.001 TRP A1097 HIS 0.003 0.001 HIS A1095 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13455) covalent geometry : angle 0.58611 / 0.30 (18311) hydrogen bonds : bond 0.02969 / 1.88 ( 232) hydrogen bonds : angle 4.49423 / 3.16 ( 675) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.498 Fit side-chains REVERT: A 410 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7386 (pp) REVERT: A 1082 TYR cc_start: 0.6797 (t80) cc_final: 0.6575 (t80) REVERT: A 1211 MET cc_start: 0.8567 (tpt) cc_final: 0.7896 (tpt) REVERT: A 1530 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8606 (mp) outliers start: 25 outliers final: 18 residues processed: 98 average time/residue: 0.0983 time to fit residues: 14.9185 Evaluate side-chains 90 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1516 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090522 restraints weight = 24206.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.091925 restraints weight = 17565.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.092699 restraints weight = 12993.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093153 restraints weight = 10333.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093219 restraints weight = 9947.776| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13455 Z= 0.129 Angle : 0.597 12.506 18311 Z= 0.308 Chirality : 0.043 0.217 1935 Planarity : 0.005 0.091 2255 Dihedral : 10.895 166.296 2113 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.90 % Favored : 88.90 % Rotamer: Outliers : 2.19 % Allowed : 18.43 % Favored : 79.38 % 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: -3.25 (0.20), residues: 1504 helix: -0.78 (0.31), residues: 304 sheet: -1.36 (0.33), residues: 257 loop : -3.06 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 924 TYR 0.011 0.001 TYR A1082 PHE 0.015 0.001 PHE A 776 TRP 0.041 0.001 TRP A1097 HIS 0.003 0.001 HIS A 931 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13455) covalent geometry : angle 0.59675 / 0.31 (18311) hydrogen bonds : bond 0.03099 / 1.96 ( 232) hydrogen bonds : angle 4.46279 / 3.13 ( 675) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.508 Fit side-chains REVERT: A 410 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7334 (pp) REVERT: A 924 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.5477 (mmt180) REVERT: A 1082 TYR cc_start: 0.6775 (t80) cc_final: 0.6569 (t80) REVERT: A 1211 MET cc_start: 0.8581 (tpt) cc_final: 0.8022 (tpt) REVERT: A 1530 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8625 (mp) outliers start: 29 outliers final: 20 residues processed: 98 average time/residue: 0.0979 time to fit residues: 14.9562 Evaluate side-chains 94 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 32 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1056 GLN A1516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.116346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087750 restraints weight = 24560.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088739 restraints weight = 18017.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089342 restraints weight = 14245.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.089714 restraints weight = 11474.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089787 restraints weight = 10713.951| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13455 Z= 0.222 Angle : 0.669 11.203 18311 Z= 0.346 Chirality : 0.046 0.235 1935 Planarity : 0.005 0.095 2255 Dihedral : 11.037 167.259 2113 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.50 % Favored : 87.30 % Rotamer: Outliers : 2.19 % Allowed : 18.66 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.20), residues: 1504 helix: -0.88 (0.31), residues: 303 sheet: -1.60 (0.31), residues: 280 loop : -3.13 (0.17), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 924 TYR 0.014 0.001 TYR A1126 PHE 0.023 0.002 PHE A 776 TRP 0.040 0.002 TRP A1097 HIS 0.005 0.001 HIS A1095 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (13455) covalent geometry : angle 0.66867 / 0.35 (18311) hydrogen bonds : bond 0.03762 / 2.39 ( 232) hydrogen bonds : angle 4.74145 / 3.34 ( 675) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.514 Fit side-chains REVERT: A 410 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7517 (pp) REVERT: A 924 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.5564 (mmt180) REVERT: A 1082 TYR cc_start: 0.6839 (t80) cc_final: 0.6441 (t80) REVERT: A 1211 MET cc_start: 0.8580 (tpt) cc_final: 0.8029 (tpt) REVERT: A 1504 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7709 (mtm-85) REVERT: A 1530 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8713 (mp) outliers start: 29 outliers final: 20 residues processed: 96 average time/residue: 0.1163 time to fit residues: 16.8279 Evaluate side-chains 92 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1504 ARG Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.0270 chunk 115 optimal weight: 6.9990 chunk 96 optimal weight: 0.0040 chunk 81 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 0.0370 overall best weight: 0.2328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 HIS A1056 GLN A1516 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.121925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093562 restraints weight = 24195.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.094654 restraints weight = 17069.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.095934 restraints weight = 12370.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095992 restraints weight = 10107.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096161 restraints weight = 9923.291| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13455 Z= 0.099 Angle : 0.573 9.933 18311 Z= 0.296 Chirality : 0.042 0.206 1935 Planarity : 0.005 0.084 2255 Dihedral : 10.844 166.105 2113 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.24 % Favored : 90.62 % Rotamer: Outliers : 1.51 % Allowed : 19.41 % Favored : 79.08 % 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: -3.08 (0.20), residues: 1504 helix: -0.59 (0.31), residues: 311 sheet: -1.26 (0.33), residues: 262 loop : -2.99 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 924 TYR 0.011 0.001 TYR A1082 PHE 0.009 0.001 PHE A1584 TRP 0.041 0.001 TRP A1097 HIS 0.003 0.001 HIS A1095 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (13455) covalent geometry : angle 0.57318 / 0.30 (18311) hydrogen bonds : bond 0.02693 / 1.70 ( 232) hydrogen bonds : angle 4.25976 / 2.99 ( 675) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 1037 MET cc_start: 0.6405 (mmm) cc_final: 0.6197 (mmm) REVERT: A 1211 MET cc_start: 0.8550 (tpt) cc_final: 0.8055 (tpt) REVERT: A 1247 ASN cc_start: 0.8057 (m-40) cc_final: 0.7211 (p0) outliers start: 20 outliers final: 16 residues processed: 97 average time/residue: 0.1027 time to fit residues: 15.3935 Evaluate side-chains 84 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 865 HIS A1056 GLN A1516 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.088332 restraints weight = 24391.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089237 restraints weight = 17072.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089763 restraints weight = 12588.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090171 restraints weight = 10678.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090410 restraints weight = 9949.915| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13455 Z= 0.208 Angle : 0.655 10.384 18311 Z= 0.336 Chirality : 0.046 0.229 1935 Planarity : 0.005 0.101 2255 Dihedral : 10.895 166.807 2113 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.84 % Favored : 87.97 % Rotamer: Outliers : 1.59 % Allowed : 19.79 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.20), residues: 1504 helix: -0.64 (0.31), residues: 303 sheet: -1.38 (0.31), residues: 283 loop : -3.04 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.013 0.001 TYR A1126 PHE 0.022 0.002 PHE A 776 TRP 0.037 0.002 TRP A1097 HIS 0.004 0.001 HIS A1095 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (13455) covalent geometry : angle 0.65458 / 0.34 (18311) hydrogen bonds : bond 0.03661 / 2.33 ( 232) hydrogen bonds : angle 4.65327 / 3.28 ( 675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.33 seconds wall clock time: 32 minutes 51.82 seconds (1971.82 seconds total)