Starting phenix.real_space_refine on Mon Dec 30 15:38:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yn9_33955/12_2024/7yn9_33955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yn9_33955/12_2024/7yn9_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_33955/12_2024/7yn9_33955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yn9_33955/12_2024/7yn9_33955.map" model { file = "/net/cci-nas-00/data/ceres_data/7yn9_33955/12_2024/7yn9_33955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yn9_33955/12_2024/7yn9_33955.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.35, per 1000 atoms: 0.72 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: 3.39 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.75 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: 5.42 Time building geometry restraints manager: 3.94 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: 7952 35.49 - 70.97: 226 70.97 - 106.45: 23 106.45 - 141.94: 0 141.94 - 177.42: 1 Dihedral angle restraints: 8202 sinusoidal: 3835 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 8199 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: 3.340 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.630 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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= 0.428 Angle : 0.830 10.399 18311 Z= 0.494 Chirality : 0.050 0.247 1935 Planarity : 0.006 0.105 2255 Dihedral : 16.329 177.424 5386 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP A1466 HIS 0.005 0.001 HIS A1313 PHE 0.023 0.002 PHE A 776 TYR 0.017 0.002 TYR A1245 ARG 0.005 0.000 ARG A 444 *********************** 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 : 1.679 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: 0.3591 time to fit residues: 55.2276 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 : 1.588 ------------------------------------------------------------------------------- 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 130 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 0.0470 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13455 Z= 0.198 Angle : 0.650 14.235 18311 Z= 0.339 Chirality : 0.044 0.222 1935 Planarity : 0.005 0.097 2255 Dihedral : 14.435 168.526 2231 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.57 % Favored : 88.23 % Rotamer: Outliers : 0.91 % Allowed : 12.61 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.18), residues: 1504 helix: -2.17 (0.29), residues: 287 sheet: -2.26 (0.31), residues: 248 loop : -3.61 (0.16), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1097 HIS 0.004 0.001 HIS A1313 PHE 0.018 0.001 PHE A 776 TYR 0.010 0.001 TYR A1126 ARG 0.005 0.000 ARG A 621 *********************** 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 96 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.522 Fit side-chains REVERT: A 86 CYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7638 (p) REVERT: A 127 GLU cc_start: 0.7426 (mp0) cc_final: 0.7189 (mp0) REVERT: A 315 TRP cc_start: 0.6390 (m100) cc_final: 0.5990 (m100) REVERT: A 601 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8183 (mttm) REVERT: A 1211 MET cc_start: 0.8330 (tpt) cc_final: 0.7919 (tpt) outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 0.2479 time to fit residues: 36.0365 Evaluate side-chains 79 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS 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 77 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 0.0770 chunk 138 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN A1056 GLN A1418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13455 Z= 0.326 Angle : 0.677 12.569 18311 Z= 0.352 Chirality : 0.046 0.235 1935 Planarity : 0.005 0.103 2255 Dihedral : 14.329 168.034 2230 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.77 % Favored : 87.03 % Rotamer: Outliers : 1.74 % Allowed : 14.73 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.19), residues: 1504 helix: -1.87 (0.29), residues: 302 sheet: -2.01 (0.31), residues: 255 loop : -3.55 (0.16), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1097 HIS 0.004 0.001 HIS A1473 PHE 0.023 0.002 PHE A 776 TYR 0.013 0.001 TYR A1276 ARG 0.004 0.000 ARG A 444 *********************** 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 100 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.671 Fit side-chains REVERT: A 127 GLU cc_start: 0.7532 (mp0) cc_final: 0.7195 (mp0) REVERT: A 315 TRP cc_start: 0.6484 (m100) cc_final: 0.6060 (m100) REVERT: A 1211 MET cc_start: 0.8435 (tpt) cc_final: 0.8009 (tpt) outliers start: 23 outliers final: 15 residues processed: 94 average time/residue: 0.2510 time to fit residues: 36.6583 Evaluate side-chains 87 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP 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 138 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1549 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= 0.203 Angle : 0.617 13.516 18311 Z= 0.319 Chirality : 0.044 0.221 1935 Planarity : 0.005 0.093 2255 Dihedral : 14.184 167.361 2229 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.84 % Favored : 88.96 % Rotamer: Outliers : 1.74 % Allowed : 16.47 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.19), residues: 1504 helix: -1.47 (0.30), residues: 304 sheet: -1.86 (0.30), residues: 264 loop : -3.37 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1097 HIS 0.003 0.001 HIS A1095 PHE 0.017 0.001 PHE A 776 TYR 0.009 0.001 TYR A1126 ARG 0.002 0.000 ARG A 621 *********************** 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 100 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.595 Fit side-chains REVERT: A 25 ARG cc_start: 0.7459 (mtm180) cc_final: 0.7259 (mtm180) REVERT: A 127 GLU cc_start: 0.7658 (mp0) cc_final: 0.7237 (mp0) REVERT: A 1130 PHE cc_start: 0.7803 (m-80) cc_final: 0.7583 (m-80) REVERT: A 1211 MET cc_start: 0.8481 (tpt) cc_final: 0.8168 (tpt) outliers start: 23 outliers final: 17 residues processed: 94 average time/residue: 0.2426 time to fit residues: 35.3268 Evaluate side-chains 89 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 485 VAL 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 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 1600 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13455 Z= 0.437 Angle : 0.722 10.319 18311 Z= 0.375 Chirality : 0.049 0.247 1935 Planarity : 0.006 0.106 2255 Dihedral : 14.281 168.057 2229 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.56 % Favored : 86.24 % Rotamer: Outliers : 2.57 % Allowed : 17.37 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.19), residues: 1504 helix: -1.55 (0.29), residues: 304 sheet: -1.99 (0.30), residues: 285 loop : -3.36 (0.17), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1097 HIS 0.004 0.001 HIS A1473 PHE 0.027 0.002 PHE A 776 TYR 0.015 0.002 TYR A1276 ARG 0.004 0.000 ARG A 444 *********************** 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 106 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 1.658 Fit side-chains REVERT: A 315 TRP cc_start: 0.6440 (m100) cc_final: 0.6041 (m100) REVERT: A 410 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7707 (pp) REVERT: A 1211 MET cc_start: 0.8491 (tpt) cc_final: 0.8239 (tpt) REVERT: A 1530 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8713 (mp) outliers start: 34 outliers final: 28 residues processed: 100 average time/residue: 0.2488 time to fit residues: 38.7161 Evaluate side-chains 100 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 184 HIS Chi-restraints excluded: chain A residue 185 ASP 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 332 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 485 VAL 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 817 VAL Chi-restraints excluded: chain A residue 948 SER 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 1436 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.9990 chunk 134 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 931 HIS A1516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1762 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= 0.156 Angle : 0.598 12.741 18311 Z= 0.310 Chirality : 0.043 0.215 1935 Planarity : 0.005 0.089 2255 Dihedral : 14.115 167.275 2229 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.84 % Favored : 88.96 % Rotamer: Outliers : 2.11 % Allowed : 18.20 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.20), residues: 1504 helix: -1.09 (0.31), residues: 303 sheet: -1.67 (0.31), residues: 268 loop : -3.21 (0.17), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1097 HIS 0.026 0.001 HIS A 184 PHE 0.014 0.001 PHE A 776 TYR 0.009 0.001 TYR A1126 ARG 0.002 0.000 ARG A1589 *********************** 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 104 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 1.554 Fit side-chains REVERT: A 410 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7504 (pp) REVERT: A 1037 MET cc_start: 0.6562 (mmm) cc_final: 0.6220 (mmm) REVERT: A 1130 PHE cc_start: 0.7861 (m-80) cc_final: 0.7625 (m-80) REVERT: A 1530 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8593 (mp) outliers start: 28 outliers final: 17 residues processed: 97 average time/residue: 0.2904 time to fit residues: 44.2262 Evaluate side-chains 91 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 185 ASP 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 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 861 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 0.0050 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A1516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13455 Z= 0.157 Angle : 0.580 13.733 18311 Z= 0.296 Chirality : 0.042 0.210 1935 Planarity : 0.005 0.092 2255 Dihedral : 13.927 166.070 2229 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.57 % Favored : 89.30 % Rotamer: Outliers : 2.04 % Allowed : 18.96 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.20), residues: 1504 helix: -0.76 (0.32), residues: 304 sheet: -1.42 (0.32), residues: 257 loop : -3.08 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A1097 HIS 0.004 0.001 HIS A 184 PHE 0.013 0.001 PHE A 776 TYR 0.016 0.001 TYR A1082 ARG 0.002 0.000 ARG A 855 *********************** 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 109 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 2.120 Fit side-chains REVERT: A 410 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7308 (pp) REVERT: A 1037 MET cc_start: 0.6584 (mmm) cc_final: 0.6256 (mmm) REVERT: A 1082 TYR cc_start: 0.6826 (t80) cc_final: 0.6624 (t80) REVERT: A 1211 MET cc_start: 0.8505 (tpt) cc_final: 0.7960 (tpt) REVERT: A 1477 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7973 (mt) REVERT: A 1530 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8586 (mp) outliers start: 27 outliers final: 16 residues processed: 104 average time/residue: 0.2455 time to fit residues: 39.8748 Evaluate side-chains 95 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 184 HIS 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 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 1477 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.0270 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A1095 HIS A1516 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13455 Z= 0.203 Angle : 0.596 11.540 18311 Z= 0.307 Chirality : 0.043 0.217 1935 Planarity : 0.005 0.088 2255 Dihedral : 13.895 166.440 2229 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.64 % Favored : 89.16 % Rotamer: Outliers : 2.49 % Allowed : 18.88 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.20), residues: 1504 helix: -0.67 (0.32), residues: 304 sheet: -1.39 (0.32), residues: 262 loop : -3.05 (0.17), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1097 HIS 0.003 0.001 HIS A 931 PHE 0.015 0.001 PHE A 776 TYR 0.010 0.001 TYR A1082 ARG 0.007 0.000 ARG A 924 *********************** 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 110 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 1.429 Fit side-chains REVERT: A 410 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7353 (pp) REVERT: A 1082 TYR cc_start: 0.6864 (t80) cc_final: 0.6613 (t80) REVERT: A 1211 MET cc_start: 0.8590 (tpt) cc_final: 0.7918 (tpt) REVERT: A 1477 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.8006 (mt) REVERT: A 1504 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7692 (mtm-85) REVERT: A 1530 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8591 (mp) outliers start: 33 outliers final: 23 residues processed: 105 average time/residue: 0.2497 time to fit residues: 40.3442 Evaluate side-chains 99 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 184 HIS 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 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 1039 VAL 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 1244 VAL Chi-restraints excluded: chain A residue 1477 LEU 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 1504 ARG 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 142 optimal weight: 4.9990 chunk 129 optimal weight: 0.0170 chunk 138 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 0.1980 chunk 130 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A1516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2227 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= 0.138 Angle : 0.575 12.936 18311 Z= 0.294 Chirality : 0.042 0.208 1935 Planarity : 0.005 0.086 2255 Dihedral : 13.822 166.174 2229 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.04 % Favored : 89.83 % Rotamer: Outliers : 2.49 % Allowed : 18.96 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.20), residues: 1504 helix: -0.52 (0.32), residues: 311 sheet: -1.23 (0.32), residues: 262 loop : -2.98 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A1097 HIS 0.013 0.001 HIS A 184 PHE 0.011 0.001 PHE A 776 TYR 0.011 0.001 TYR A1082 ARG 0.008 0.000 ARG A 924 *********************** 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 110 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 1.608 Fit side-chains REVERT: A 924 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5732 (mmt180) REVERT: A 1082 TYR cc_start: 0.6852 (t80) cc_final: 0.6601 (t80) REVERT: A 1211 MET cc_start: 0.8471 (tpt) cc_final: 0.7966 (tpt) REVERT: A 1247 ASN cc_start: 0.8046 (m-40) cc_final: 0.7207 (p0) REVERT: A 1530 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8580 (mp) outliers start: 33 outliers final: 22 residues processed: 105 average time/residue: 0.2279 time to fit residues: 37.5992 Evaluate side-chains 96 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 234 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 517 PHE 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 1039 VAL 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 1185 THR Chi-restraints excluded: chain A residue 1244 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 12 optimal weight: 0.0040 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A1516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2341 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= 0.143 Angle : 0.567 11.125 18311 Z= 0.289 Chirality : 0.042 0.208 1935 Planarity : 0.004 0.085 2255 Dihedral : 13.728 165.861 2229 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.97 % Favored : 89.89 % Rotamer: Outliers : 2.11 % Allowed : 19.41 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.21), residues: 1504 helix: -0.36 (0.32), residues: 311 sheet: -0.97 (0.32), residues: 265 loop : -2.92 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1097 HIS 0.003 0.001 HIS A1095 PHE 0.011 0.001 PHE A 776 TYR 0.011 0.001 TYR A1082 ARG 0.007 0.000 ARG A 924 ********************** 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 108 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 1.492 Fit side-chains REVERT: A 127 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: A 1247 ASN cc_start: 0.8075 (m-40) cc_final: 0.7244 (p0) REVERT: A 1278 LYS cc_start: 0.8822 (tttt) cc_final: 0.8543 (ttmm) REVERT: A 1530 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8591 (mp) outliers start: 28 outliers final: 21 residues processed: 104 average time/residue: 0.2472 time to fit residues: 39.9145 Evaluate side-chains 97 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 127 GLU 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 517 PHE 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 1039 VAL 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 1185 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1485 LEU 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 130 optimal weight: 0.0020 chunk 37 optimal weight: 0.0030 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3678 r_free = 0.3678 target = 0.123099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094944 restraints weight = 24095.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.095919 restraints weight = 16964.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.097234 restraints weight = 12576.107| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2521 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= 0.134 Angle : 0.555 10.133 18311 Z= 0.284 Chirality : 0.041 0.206 1935 Planarity : 0.004 0.083 2255 Dihedral : 13.635 165.624 2229 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.38 % Favored : 90.49 % Rotamer: Outliers : 1.81 % Allowed : 19.86 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.21), residues: 1504 helix: -0.14 (0.32), residues: 311 sheet: -0.87 (0.32), residues: 270 loop : -2.88 (0.18), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1097 HIS 0.005 0.001 HIS A1095 PHE 0.010 0.001 PHE A 776 TYR 0.007 0.001 TYR A 492 ARG 0.003 0.000 ARG A 924 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2418.31 seconds wall clock time: 45 minutes 31.53 seconds (2731.53 seconds total)