Starting phenix.real_space_refine on Fri Sep 11 22:54:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ela_31178/09_2026/7ela_31178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ela_31178/09_2026/7ela_31178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ela_31178/09_2026/7ela_31178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ela_31178/09_2026/7ela_31178.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ela_31178/09_2026/7ela_31178.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ela_31178/09_2026/7ela_31178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ela_31178/09_2026/7ela_31178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ela_31178/09_2026/7ela_31178.map" } resolution = 3.4 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= 0.003 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: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 P 7 5.49 5 S 80 5.16 5 C 7497 2.51 5 N 1978 2.21 5 O 2226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11791 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 375 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 3} Chain: "A" Number of atoms: 11264 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1402, 11250 Classifications: {'peptide': 1402} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 46, 'TRANS': 1355} Chain breaks: 11 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 1402, 11250 Classifications: {'peptide': 1402} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 46, 'TRANS': 1355} Chain breaks: 11 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 11448 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 55 SG CYS B 31 75.022 70.911 96.200 1.00 59.29 S ATOM 76 SG CYS B 34 77.728 67.648 96.289 1.00 53.18 S ATOM 207 SG CYS B 50 77.976 71.670 97.807 1.00 71.19 S ATOM 229 SG CYS B 53 77.915 71.242 94.375 1.00 71.71 S ATOM 155 SG CYS B 44 70.342 79.282 92.118 1.00 81.15 S ATOM 308 SG CYS B 64 72.367 77.979 89.642 1.00 84.11 S ATOM 329 SG CYS B 67 69.032 78.503 89.041 1.00 90.04 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A1392 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A1392 " occ=0.50 Time building chain proxies: 4.35, per 1000 atoms: 0.37 Number of scatterers: 11791 At special positions: 0 Unit cell: (115, 99, 122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 80 16.00 P 7 15.00 O 2226 8.00 N 1978 7.00 C 7497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1692 " - pdb=" SG CYS A1792 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 896.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 53 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 50 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 31 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 34 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 47 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 67 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 44 " Number of angles added : 9 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 13 sheets defined 55.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 34 through 59 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 108 through 132 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 211 through 221 removed outlier: 4.130A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 252 removed outlier: 3.776A pdb=" N LYS A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 340 through 363 removed outlier: 3.659A pdb=" N ARG A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.872A pdb=" N VAL A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 436 Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.518A pdb=" N LYS A 445 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'A' and resid 588 through 603 removed outlier: 3.850A pdb=" N GLN A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 603 " --> pdb=" O MET A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 removed outlier: 4.393A pdb=" N ASN A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 612 through 630 Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.697A pdb=" N VAL A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 670 through 686 Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 708 through 711 Processing helix chain 'A' and resid 717 through 737 Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.607A pdb=" N LEU A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 795 Processing helix chain 'A' and resid 1139 through 1160 Processing helix chain 'A' and resid 1167 through 1184 Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 3.534A pdb=" N MET A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A1200 " --> pdb=" O TRP A1196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1195 through 1200' Processing helix chain 'A' and resid 1201 through 1211 Processing helix chain 'A' and resid 1225 through 1238 Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1269 through 1280 Processing helix chain 'A' and resid 1299 through 1323 Processing helix chain 'A' and resid 1340 through 1350 Processing helix chain 'A' and resid 1350 through 1368 Processing helix chain 'A' and resid 1398 through 1409 removed outlier: 3.530A pdb=" N PHE A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1433 Processing helix chain 'A' and resid 1435 through 1453 removed outlier: 3.581A pdb=" N ALA A1453 " --> pdb=" O LEU A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1490 through 1508 removed outlier: 3.573A pdb=" N LYS A1494 " --> pdb=" O ASP A1490 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A1508 " --> pdb=" O ASN A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1520 removed outlier: 3.732A pdb=" N THR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1536 removed outlier: 3.905A pdb=" N LYS A1529 " --> pdb=" O LEU A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1586 removed outlier: 3.814A pdb=" N ILE A1586 " --> pdb=" O ILE A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1626 Processing helix chain 'A' and resid 1640 through 1650 Processing helix chain 'A' and resid 1678 through 1681 Processing helix chain 'A' and resid 1686 through 1701 Processing helix chain 'A' and resid 1703 through 1707 Processing helix chain 'A' and resid 1744 through 1753 Processing helix chain 'A' and resid 1753 through 1759 Processing helix chain 'A' and resid 1782 through 1791 removed outlier: 4.281A pdb=" N ASP A1789 " --> pdb=" O CYS A1785 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A1790 " --> pdb=" O VAL A1786 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN A1791 " --> pdb=" O ALA A1787 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1819 removed outlier: 3.590A pdb=" N ARG A1818 " --> pdb=" O SER A1814 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A1819 " --> pdb=" O SER A1815 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1814 through 1819' Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 6.552A pdb=" N LEU A 98 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.471A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 208 removed outlier: 6.152A pdb=" N LEU A 207 " --> pdb=" O TYR A1109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 542 removed outlier: 6.411A pdb=" N LYS A 560 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR A 576 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR A 562 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER A 574 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 564 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1133 through 1138 removed outlier: 3.584A pdb=" N LEU A1123 " --> pdb=" O GLU A1242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1383 through 1385 Processing sheet with id=AB1, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AB2, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.539A pdb=" N VAL A1631 " --> pdb=" O LEU A1639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1710 through 1711 Processing sheet with id=AB4, first strand: chain 'A' and resid 1725 through 1728 removed outlier: 3.709A pdb=" N VAL A1812 " --> pdb=" O PHE A1726 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3623 1.34 - 1.46: 1716 1.46 - 1.57: 6562 1.57 - 1.69: 13 1.69 - 1.81: 117 Bond restraints: 12031 Sorted by residual: bond pdb=" N VAL A1468 " pdb=" CA VAL A1468 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.40e+00 bond pdb=" N THR A1466 " pdb=" CA THR A1466 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.34e-02 5.57e+03 6.94e+00 bond pdb=" N ARG A1469 " pdb=" CA ARG A1469 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.14e-02 7.69e+03 5.95e+00 bond pdb=" N GLU A1465 " pdb=" CA GLU A1465 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.25e-02 6.40e+03 5.12e+00 bond pdb=" N ASP A1467 " pdb=" CA ASP A1467 " ideal model delta sigma weight residual 1.460 1.487 -0.028 1.50e-02 4.44e+03 3.41e+00 ... (remaining 12026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 15924 1.68 - 3.36: 299 3.36 - 5.04: 45 5.04 - 6.72: 10 6.72 - 8.40: 4 Bond angle restraints: 16282 Sorted by residual: angle pdb=" N ARG A1469 " pdb=" CA ARG A1469 " pdb=" C ARG A1469 " ideal model delta sigma weight residual 114.62 106.22 8.40 1.14e+00 7.69e-01 5.43e+01 angle pdb=" CA ARG A1469 " pdb=" C ARG A1469 " pdb=" N ASP A1470 " ideal model delta sigma weight residual 119.71 114.52 5.19 1.17e+00 7.31e-01 1.97e+01 angle pdb=" CA ASP A1467 " pdb=" C ASP A1467 " pdb=" O ASP A1467 " ideal model delta sigma weight residual 121.78 117.58 4.20 1.12e+00 7.97e-01 1.41e+01 angle pdb=" O ARG A1469 " pdb=" C ARG A1469 " pdb=" N ASP A1470 " ideal model delta sigma weight residual 121.67 125.93 -4.26 1.30e+00 5.92e-01 1.07e+01 angle pdb=" CA THR A1466 " pdb=" C THR A1466 " pdb=" O THR A1466 " ideal model delta sigma weight residual 121.87 118.25 3.62 1.16e+00 7.43e-01 9.76e+00 ... (remaining 16277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 6570 17.79 - 35.58: 538 35.58 - 53.36: 136 53.36 - 71.15: 36 71.15 - 88.94: 21 Dihedral angle restraints: 7301 sinusoidal: 3023 harmonic: 4278 Sorted by residual: dihedral pdb=" C4' U C 14 " pdb=" C3' U C 14 " pdb=" C2' U C 14 " pdb=" C1' U C 14 " ideal model delta sinusoidal sigma weight residual 36.34 -35.73 72.07 1 3.10e+00 1.04e-01 6.91e+02 dihedral pdb=" C4' C C 18 " pdb=" C3' C C 18 " pdb=" C2' C C 18 " pdb=" C1' C C 18 " ideal model delta sinusoidal sigma weight residual 36.34 -34.66 71.00 1 3.10e+00 1.04e-01 6.74e+02 dihedral pdb=" C4' U C 16 " pdb=" C3' U C 16 " pdb=" C2' U C 16 " pdb=" C1' U C 16 " ideal model delta sinusoidal sigma weight residual 36.34 -34.31 70.66 1 3.10e+00 1.04e-01 6.68e+02 ... (remaining 7298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1609 0.055 - 0.111: 214 0.111 - 0.166: 25 0.166 - 0.221: 3 0.221 - 0.276: 11 Chirality restraints: 1862 Sorted by residual: chirality pdb=" C2' U C 16 " pdb=" C3' U C 16 " pdb=" O2' U C 16 " pdb=" C1' U C 16 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' U C 14 " pdb=" C4' U C 14 " pdb=" O3' U C 14 " pdb=" C2' U C 14 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' C C 18 " pdb=" C3' C C 18 " pdb=" O2' C C 18 " pdb=" C1' C C 18 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1859 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1396 " -0.023 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A1397 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1397 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1397 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 152 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 153 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G C 15 " 0.017 2.00e-02 2.50e+03 8.07e-03 1.95e+00 pdb=" N9 G C 15 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G C 15 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 15 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G C 15 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G C 15 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G C 15 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G C 15 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G C 15 " 0.000 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 338 2.70 - 3.25: 12378 3.25 - 3.80: 19086 3.80 - 4.35: 25075 4.35 - 4.90: 41330 Nonbonded interactions: 98207 Sorted by model distance: nonbonded pdb=" N ASP A1470 " pdb=" OD1 ASP A1470 " model vdw 2.153 3.120 nonbonded pdb=" O GLY A 683 " pdb=" OG SER A 687 " model vdw 2.212 3.040 nonbonded pdb=" O ASP A1490 " pdb=" OG SER A1493 " model vdw 2.231 3.040 nonbonded pdb=" O PRO A1459 " pdb=" NE2 GLN A1483 " model vdw 2.237 3.120 nonbonded pdb=" O SER A1373 " pdb=" OG SER A1376 " model vdw 2.238 3.040 ... (remaining 98202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.160 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.004 0.221 12040 Z= 0.164 Angle : 0.712 20.428 16293 Z= 0.333 Chirality : 0.044 0.276 1862 Planarity : 0.003 0.036 2028 Dihedral : 15.240 88.940 4514 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.79 % Allowed : 8.60 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.20), residues: 1428 helix: -0.47 (0.17), residues: 773 sheet: -2.02 (0.49), residues: 91 loop : -3.56 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 380 TYR 0.012 0.001 TYR A 302 PHE 0.014 0.001 PHE A 541 TRP 0.010 0.001 TRP A1666 HIS 0.006 0.001 HIS A1744 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (12031) covalent geometry : angle 0.58415 / 0.32 (16282) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 1.52202 / 0.80 ( 2) hydrogen bonds : bond 0.13202 / 7.91 ( 606) hydrogen bonds : angle 5.41012 / 3.61 ( 1764) metal coordination : bond 0.09884 / 5.81 ( 8) metal coordination : angle 17.32551 / 14.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 50 CYS cc_start: 0.6258 (p) cc_final: 0.5815 (p) REVERT: B 53 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7744 (m) REVERT: A 343 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7406 (mmtm) REVERT: A 385 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: A 669 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7337 (p0) REVERT: A 751 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 755 MET cc_start: 0.8687 (tpp) cc_final: 0.8446 (tpp) REVERT: A 1180 LEU cc_start: 0.8675 (tp) cc_final: 0.8399 (tp) REVERT: A 1223 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.5590 (tp) REVERT: A 1366 ASP cc_start: 0.8442 (t70) cc_final: 0.7819 (t0) REVERT: A 1368 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7324 (mt) REVERT: A 1467 ASP cc_start: 0.6909 (p0) cc_final: 0.6509 (p0) REVERT: A 1469 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6387 (tpm170) REVERT: A 1546 GLU cc_start: 0.7048 (pt0) cc_final: 0.6847 (pt0) REVERT: A 1579 ILE cc_start: 0.3824 (OUTLIER) cc_final: 0.3028 (tp) REVERT: A 1810 TYR cc_start: 0.8148 (m-80) cc_final: 0.7741 (m-80) outliers start: 37 outliers final: 23 residues processed: 268 average time/residue: 0.1070 time to fit residues: 40.6356 Evaluate side-chains 193 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1469 ARG Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1639 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN A 58 ASN A 114 GLN A 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS A 290 GLN A 360 GLN A 567 ASN A 593 GLN A 607 ASN A 655 HIS A 703 ASN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN A1128 GLN A1132 ASN A1167 ASN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 HIS ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 ASN A1335 GLN A1443 GLN A1483 GLN A1524 HIS A1530 ASN A1587 GLN A1664 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138425 restraints weight = 20528.980| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.67 r_work: 0.3090 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12040 Z= 0.171 Angle : 0.711 13.683 16293 Z= 0.339 Chirality : 0.052 0.671 1862 Planarity : 0.004 0.047 2028 Dihedral : 8.788 84.466 1703 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.70 % Allowed : 12.38 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.22), residues: 1428 helix: 0.45 (0.18), residues: 794 sheet: -1.52 (0.53), residues: 89 loop : -3.19 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 63 TYR 0.025 0.002 TYR A1125 PHE 0.016 0.002 PHE A 541 TRP 0.012 0.002 TRP A 394 HIS 0.010 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (12031) covalent geometry : angle 0.70476 / 0.34 (16282) SS BOND : bond 0.00705 / 0.37 ( 1) SS BOND : angle 2.35270 / 1.25 ( 2) hydrogen bonds : bond 0.03911 / 2.40 ( 606) hydrogen bonds : angle 4.40768 / 2.90 ( 1764) metal coordination : bond 0.00661 / 0.48 ( 8) metal coordination : angle 3.97189 / 3.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 113 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6232 (mm-30) REVERT: A 347 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8895 (mp) REVERT: A 360 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8169 (pp30) REVERT: A 384 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8870 (tt) REVERT: A 647 MET cc_start: 0.8813 (tpt) cc_final: 0.8452 (tpt) REVERT: A 669 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7865 (p0) REVERT: A 1150 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: A 1180 LEU cc_start: 0.8950 (tp) cc_final: 0.8701 (tp) REVERT: A 1311 GLU cc_start: 0.8050 (tp30) cc_final: 0.7547 (tp30) REVERT: A 1366 ASP cc_start: 0.8893 (t70) cc_final: 0.8370 (t0) REVERT: A 1368 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8097 (mt) REVERT: A 1467 ASP cc_start: 0.8049 (p0) cc_final: 0.7586 (p0) REVERT: A 1546 GLU cc_start: 0.7740 (pt0) cc_final: 0.7385 (pt0) REVERT: A 1654 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7842 (mm) REVERT: A 1810 TYR cc_start: 0.8009 (m-80) cc_final: 0.7626 (m-80) outliers start: 49 outliers final: 23 residues processed: 214 average time/residue: 0.1004 time to fit residues: 31.4935 Evaluate side-chains 195 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 92 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 HIS A1296 GLN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1530 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.178526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138684 restraints weight = 19284.227| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.09 r_work: 0.3190 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12040 Z= 0.157 Angle : 0.653 13.563 16293 Z= 0.315 Chirality : 0.046 0.453 1862 Planarity : 0.004 0.047 2028 Dihedral : 7.969 84.992 1681 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.62 % Allowed : 14.64 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1428 helix: 0.86 (0.18), residues: 791 sheet: -1.65 (0.52), residues: 101 loop : -2.99 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1469 TYR 0.017 0.001 TYR A1125 PHE 0.018 0.001 PHE A 541 TRP 0.019 0.002 TRP A 369 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (12031) covalent geometry : angle 0.64667 / 0.31 (16282) SS BOND : bond 0.00154 / 0.08 ( 1) SS BOND : angle 2.21069 / 1.17 ( 2) hydrogen bonds : bond 0.03691 / 2.27 ( 606) hydrogen bonds : angle 4.27772 / 2.80 ( 1764) metal coordination : bond 0.00600 / 0.38 ( 8) metal coordination : angle 3.79409 / 3.03 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6273 (mm-30) REVERT: A 268 ASN cc_start: 0.7882 (m-40) cc_final: 0.7531 (t0) REVERT: A 388 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8237 (mttt) REVERT: A 399 GLN cc_start: 0.8041 (tt0) cc_final: 0.7741 (tm-30) REVERT: A 622 MET cc_start: 0.9063 (mtm) cc_final: 0.8857 (mtm) REVERT: A 647 MET cc_start: 0.8863 (tpt) cc_final: 0.8420 (tpt) REVERT: A 669 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7787 (p0) REVERT: A 1150 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: A 1253 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7597 (mtmm) REVERT: A 1276 TYR cc_start: 0.8878 (m-10) cc_final: 0.8485 (m-10) REVERT: A 1311 GLU cc_start: 0.8018 (tp30) cc_final: 0.7516 (tp30) REVERT: A 1366 ASP cc_start: 0.8845 (t70) cc_final: 0.8323 (t0) REVERT: A 1467 ASP cc_start: 0.8129 (p0) cc_final: 0.7594 (p0) REVERT: A 1546 GLU cc_start: 0.7617 (pt0) cc_final: 0.7182 (pt0) REVERT: A 1654 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7795 (mm) REVERT: A 1701 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8037 (pp) REVERT: A 1810 TYR cc_start: 0.7972 (m-80) cc_final: 0.7559 (m-80) outliers start: 48 outliers final: 33 residues processed: 209 average time/residue: 0.1083 time to fit residues: 33.3123 Evaluate side-chains 196 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1639 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 636 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.179060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128786 restraints weight = 28108.423| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.09 r_work: 0.3163 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12040 Z= 0.145 Angle : 0.639 13.492 16293 Z= 0.309 Chirality : 0.044 0.404 1862 Planarity : 0.004 0.050 2028 Dihedral : 7.818 78.876 1679 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.77 % Allowed : 15.40 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.22), residues: 1428 helix: 1.10 (0.18), residues: 791 sheet: -1.22 (0.55), residues: 89 loop : -2.89 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1469 TYR 0.020 0.001 TYR A 148 PHE 0.016 0.001 PHE A 541 TRP 0.016 0.002 TRP A 394 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (12031) covalent geometry : angle 0.63256 / 0.31 (16282) SS BOND : bond 0.00436 / 0.23 ( 1) SS BOND : angle 3.01941 / 1.59 ( 2) hydrogen bonds : bond 0.03545 / 2.20 ( 606) hydrogen bonds : angle 4.19119 / 2.76 ( 1764) metal coordination : bond 0.00680 / 0.40 ( 8) metal coordination : angle 3.66344 / 2.96 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.7865 (m-40) cc_final: 0.7592 (t0) REVERT: A 388 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8369 (mttt) REVERT: A 456 TYR cc_start: 0.7711 (t80) cc_final: 0.7451 (t80) REVERT: A 647 MET cc_start: 0.8810 (tpt) cc_final: 0.8313 (tpt) REVERT: A 669 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7786 (p0) REVERT: A 751 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 1150 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: A 1253 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7682 (mtmm) REVERT: A 1276 TYR cc_start: 0.8862 (m-10) cc_final: 0.8445 (m-10) REVERT: A 1311 GLU cc_start: 0.7971 (tp30) cc_final: 0.7475 (tp30) REVERT: A 1366 ASP cc_start: 0.8683 (t70) cc_final: 0.8181 (t0) REVERT: A 1368 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8151 (mt) REVERT: A 1467 ASP cc_start: 0.8122 (p0) cc_final: 0.7623 (p0) REVERT: A 1546 GLU cc_start: 0.7608 (pt0) cc_final: 0.7057 (pt0) REVERT: A 1654 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7779 (mm) REVERT: A 1667 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6746 (ptm160) REVERT: A 1810 TYR cc_start: 0.8013 (m-80) cc_final: 0.7612 (m-80) outliers start: 50 outliers final: 34 residues processed: 209 average time/residue: 0.1121 time to fit residues: 34.1497 Evaluate side-chains 198 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1639 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1667 ARG Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 106 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 131 optimal weight: 0.0010 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141180 restraints weight = 23936.837| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 4.58 r_work: 0.3137 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12040 Z= 0.120 Angle : 0.619 12.701 16293 Z= 0.299 Chirality : 0.042 0.368 1862 Planarity : 0.004 0.049 2028 Dihedral : 7.576 75.162 1677 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.85 % Allowed : 15.32 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.23), residues: 1428 helix: 1.28 (0.18), residues: 790 sheet: -0.88 (0.60), residues: 79 loop : -2.87 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.016 0.001 TYR A1125 PHE 0.014 0.001 PHE A 541 TRP 0.028 0.001 TRP A 394 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12031) covalent geometry : angle 0.61043 / 0.30 (16282) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 2.20198 / 1.16 ( 2) hydrogen bonds : bond 0.03408 / 2.11 ( 606) hydrogen bonds : angle 4.09712 / 2.71 ( 1764) metal coordination : bond 0.01954 / 1.04 ( 8) metal coordination : angle 4.22821 / 3.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: B 34 CYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7174 (m) REVERT: B 53 CYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7380 (m) REVERT: A 264 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.8065 (m-40) REVERT: A 268 ASN cc_start: 0.7801 (m-40) cc_final: 0.7514 (t0) REVERT: A 343 LYS cc_start: 0.7767 (mmtm) cc_final: 0.7317 (mmtm) REVERT: A 347 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8810 (mp) REVERT: A 388 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8359 (mttt) REVERT: A 456 TYR cc_start: 0.7686 (t80) cc_final: 0.7320 (t80) REVERT: A 622 MET cc_start: 0.9037 (mtm) cc_final: 0.8834 (mtm) REVERT: A 640 GLN cc_start: 0.8324 (mt0) cc_final: 0.8095 (mt0) REVERT: A 647 MET cc_start: 0.8887 (tpt) cc_final: 0.8425 (tpt) REVERT: A 669 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7896 (p0) REVERT: A 1150 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: A 1253 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7625 (mtmm) REVERT: A 1276 TYR cc_start: 0.8833 (m-10) cc_final: 0.8520 (m-10) REVERT: A 1311 GLU cc_start: 0.8067 (tp30) cc_final: 0.7580 (tp30) REVERT: A 1366 ASP cc_start: 0.8810 (t70) cc_final: 0.8297 (t0) REVERT: A 1368 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8058 (mt) REVERT: A 1467 ASP cc_start: 0.8220 (p0) cc_final: 0.7658 (p0) REVERT: A 1546 GLU cc_start: 0.7680 (pt0) cc_final: 0.7126 (pt0) REVERT: A 1654 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7798 (mm) REVERT: A 1667 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6541 (ptm160) REVERT: A 1810 TYR cc_start: 0.7885 (m-80) cc_final: 0.7539 (m-80) outliers start: 51 outliers final: 31 residues processed: 218 average time/residue: 0.1104 time to fit residues: 34.8674 Evaluate side-chains 200 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1490 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1667 ARG Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 399 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.178934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128866 restraints weight = 25528.915| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.96 r_work: 0.3166 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12040 Z= 0.150 Angle : 0.628 11.516 16293 Z= 0.304 Chirality : 0.043 0.364 1862 Planarity : 0.004 0.046 2028 Dihedral : 7.572 73.073 1677 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.62 % Allowed : 15.85 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.23), residues: 1428 helix: 1.33 (0.18), residues: 790 sheet: -1.33 (0.57), residues: 80 loop : -2.74 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1469 TYR 0.016 0.001 TYR A1125 PHE 0.022 0.001 PHE A 583 TRP 0.030 0.002 TRP A 394 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (12031) covalent geometry : angle 0.62122 / 0.30 (16282) SS BOND : bond 0.00338 / 0.18 ( 1) SS BOND : angle 2.10755 / 1.11 ( 2) hydrogen bonds : bond 0.03533 / 2.19 ( 606) hydrogen bonds : angle 4.14505 / 2.74 ( 1764) metal coordination : bond 0.01221 / 0.64 ( 8) metal coordination : angle 3.92280 / 3.15 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 CYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7064 (m) REVERT: B 53 CYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7347 (m) REVERT: A 360 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8556 (pp30) REVERT: A 388 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8403 (mttt) REVERT: A 456 TYR cc_start: 0.7581 (t80) cc_final: 0.7178 (t80) REVERT: A 647 MET cc_start: 0.8882 (tpt) cc_final: 0.8217 (tpt) REVERT: A 660 ASP cc_start: 0.8226 (t0) cc_final: 0.8009 (t0) REVERT: A 669 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7793 (p0) REVERT: A 751 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7888 (tm-30) REVERT: A 1150 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: A 1223 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.5919 (mm) REVERT: A 1253 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7666 (mtmm) REVERT: A 1276 TYR cc_start: 0.8831 (m-10) cc_final: 0.8511 (m-10) REVERT: A 1311 GLU cc_start: 0.7993 (tp30) cc_final: 0.7505 (tp30) REVERT: A 1366 ASP cc_start: 0.8688 (t70) cc_final: 0.8201 (t0) REVERT: A 1467 ASP cc_start: 0.8169 (p0) cc_final: 0.7710 (p0) REVERT: A 1546 GLU cc_start: 0.7599 (pt0) cc_final: 0.7210 (pt0) REVERT: A 1810 TYR cc_start: 0.8004 (m-80) cc_final: 0.7610 (m-80) outliers start: 48 outliers final: 36 residues processed: 204 average time/residue: 0.1025 time to fit residues: 30.5118 Evaluate side-chains 205 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1490 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 0.0040 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 138 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1635 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130130 restraints weight = 27192.117| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.11 r_work: 0.3183 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12040 Z= 0.137 Angle : 0.622 11.121 16293 Z= 0.301 Chirality : 0.042 0.353 1862 Planarity : 0.004 0.044 2028 Dihedral : 7.435 71.365 1675 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.47 % Allowed : 16.53 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1428 helix: 1.37 (0.18), residues: 788 sheet: -0.96 (0.62), residues: 70 loop : -2.75 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1469 TYR 0.017 0.001 TYR A1125 PHE 0.020 0.001 PHE A 583 TRP 0.025 0.001 TRP A 394 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (12031) covalent geometry : angle 0.61552 / 0.30 (16282) SS BOND : bond 0.00399 / 0.21 ( 1) SS BOND : angle 1.75172 / 0.92 ( 2) hydrogen bonds : bond 0.03475 / 2.15 ( 606) hydrogen bonds : angle 4.10863 / 2.72 ( 1764) metal coordination : bond 0.01041 / 0.54 ( 8) metal coordination : angle 3.86099 / 3.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 CYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6931 (m) REVERT: B 53 CYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7285 (m) REVERT: B 60 VAL cc_start: 0.7787 (OUTLIER) cc_final: 0.7183 (t) REVERT: A 388 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8401 (mttt) REVERT: A 420 ASN cc_start: 0.8601 (t0) cc_final: 0.8307 (t0) REVERT: A 456 TYR cc_start: 0.7676 (t80) cc_final: 0.7236 (t80) REVERT: A 647 MET cc_start: 0.8868 (tpt) cc_final: 0.8208 (tpt) REVERT: A 660 ASP cc_start: 0.8232 (t0) cc_final: 0.8015 (t0) REVERT: A 669 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7762 (p0) REVERT: A 694 MET cc_start: 0.8865 (tpt) cc_final: 0.8410 (tpt) REVERT: A 1223 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.5934 (mm) REVERT: A 1253 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7667 (mtmm) REVERT: A 1276 TYR cc_start: 0.8828 (m-10) cc_final: 0.8511 (m-10) REVERT: A 1311 GLU cc_start: 0.7976 (tp30) cc_final: 0.7497 (tp30) REVERT: A 1366 ASP cc_start: 0.8667 (t70) cc_final: 0.8176 (t0) REVERT: A 1368 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8079 (mt) REVERT: A 1467 ASP cc_start: 0.8152 (p0) cc_final: 0.7662 (p0) REVERT: A 1546 GLU cc_start: 0.7516 (pt0) cc_final: 0.7088 (pt0) REVERT: A 1667 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6699 (ptm160) REVERT: A 1810 TYR cc_start: 0.7977 (m-80) cc_final: 0.7614 (m-80) outliers start: 46 outliers final: 32 residues processed: 212 average time/residue: 0.1050 time to fit residues: 32.4531 Evaluate side-chains 201 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1490 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1667 ARG Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 0.0010 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 132 optimal weight: 0.0670 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 399 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1210 GLN ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.181532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141118 restraints weight = 19645.234| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.18 r_work: 0.3219 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12040 Z= 0.122 Angle : 0.613 10.053 16293 Z= 0.298 Chirality : 0.042 0.332 1862 Planarity : 0.004 0.044 2028 Dihedral : 7.300 68.675 1674 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.02 % Allowed : 17.13 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1428 helix: 1.40 (0.18), residues: 789 sheet: -0.93 (0.62), residues: 70 loop : -2.66 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1469 TYR 0.016 0.001 TYR A1125 PHE 0.019 0.001 PHE A 583 TRP 0.024 0.001 TRP A 394 HIS 0.003 0.001 HIS A1361 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (12031) covalent geometry : angle 0.60754 / 0.30 (16282) SS BOND : bond 0.00484 / 0.25 ( 1) SS BOND : angle 1.45572 / 0.77 ( 2) hydrogen bonds : bond 0.03354 / 2.07 ( 606) hydrogen bonds : angle 4.04369 / 2.68 ( 1764) metal coordination : bond 0.00802 / 0.42 ( 8) metal coordination : angle 3.52968 / 2.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 CYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7110 (m) REVERT: B 53 CYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7371 (m) REVERT: B 60 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7171 (t) REVERT: A 37 MET cc_start: 0.6161 (tpp) cc_final: 0.5899 (tpp) REVERT: A 360 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8044 (pp30) REVERT: A 420 ASN cc_start: 0.8652 (t0) cc_final: 0.8373 (t0) REVERT: A 456 TYR cc_start: 0.7590 (t80) cc_final: 0.7192 (t80) REVERT: A 647 MET cc_start: 0.8855 (tpt) cc_final: 0.8311 (tpt) REVERT: A 660 ASP cc_start: 0.8332 (t0) cc_final: 0.8071 (t0) REVERT: A 669 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7825 (p0) REVERT: A 694 MET cc_start: 0.8871 (tpt) cc_final: 0.8435 (tpt) REVERT: A 1150 GLU cc_start: 0.8338 (mp0) cc_final: 0.8077 (mp0) REVERT: A 1223 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6001 (mm) REVERT: A 1253 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7612 (mtmm) REVERT: A 1276 TYR cc_start: 0.8821 (m-10) cc_final: 0.8524 (m-10) REVERT: A 1311 GLU cc_start: 0.8011 (tp30) cc_final: 0.7512 (tp30) REVERT: A 1366 ASP cc_start: 0.8672 (t70) cc_final: 0.8178 (t0) REVERT: A 1368 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8036 (mt) REVERT: A 1467 ASP cc_start: 0.8157 (p0) cc_final: 0.7622 (p0) REVERT: A 1546 GLU cc_start: 0.7535 (pt0) cc_final: 0.7128 (pt0) REVERT: A 1667 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6699 (ptm160) REVERT: A 1810 TYR cc_start: 0.7885 (m-80) cc_final: 0.7562 (m-80) outliers start: 40 outliers final: 25 residues processed: 209 average time/residue: 0.1063 time to fit residues: 31.9701 Evaluate side-chains 197 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1490 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1667 ARG Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 290 GLN A 443 HIS ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141577 restraints weight = 18619.272| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.99 r_work: 0.3182 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 12040 Z= 0.168 Angle : 0.892 59.196 16293 Z= 0.487 Chirality : 0.043 0.409 1862 Planarity : 0.004 0.044 2028 Dihedral : 7.225 68.668 1670 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.64 % Allowed : 17.89 % Favored : 79.47 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1428 helix: 1.42 (0.18), residues: 790 sheet: -0.98 (0.61), residues: 70 loop : -2.66 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1133 TYR 0.016 0.001 TYR A1125 PHE 0.017 0.001 PHE A 583 TRP 0.017 0.001 TRP A 394 HIS 0.006 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (12031) covalent geometry : angle 0.88831 / 0.49 (16282) SS BOND : bond 0.00488 / 0.26 ( 1) SS BOND : angle 1.36852 / 0.73 ( 2) hydrogen bonds : bond 0.03365 / 2.08 ( 606) hydrogen bonds : angle 4.04408 / 2.68 ( 1764) metal coordination : bond 0.00809 / 0.42 ( 8) metal coordination : angle 3.52440 / 2.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 CYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7127 (m) REVERT: B 53 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7401 (m) REVERT: B 60 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7167 (t) REVERT: A 37 MET cc_start: 0.6171 (tpp) cc_final: 0.5910 (tpp) REVERT: A 420 ASN cc_start: 0.8632 (t0) cc_final: 0.8352 (t0) REVERT: A 456 TYR cc_start: 0.7586 (t80) cc_final: 0.7224 (t80) REVERT: A 647 MET cc_start: 0.8807 (tpt) cc_final: 0.8263 (tpt) REVERT: A 660 ASP cc_start: 0.8259 (t0) cc_final: 0.8001 (t0) REVERT: A 669 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7828 (p0) REVERT: A 694 MET cc_start: 0.8833 (tpt) cc_final: 0.8417 (tpt) REVERT: A 1150 GLU cc_start: 0.8307 (mp0) cc_final: 0.8026 (mp0) REVERT: A 1223 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6003 (mm) REVERT: A 1253 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7650 (mtmm) REVERT: A 1276 TYR cc_start: 0.8813 (m-10) cc_final: 0.8508 (m-10) REVERT: A 1311 GLU cc_start: 0.7996 (tp30) cc_final: 0.7481 (tp30) REVERT: A 1366 ASP cc_start: 0.8618 (t70) cc_final: 0.8120 (t0) REVERT: A 1368 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8043 (mt) REVERT: A 1467 ASP cc_start: 0.8131 (p0) cc_final: 0.7647 (p0) REVERT: A 1546 GLU cc_start: 0.7529 (pt0) cc_final: 0.7127 (pt0) REVERT: A 1667 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6702 (ptm160) REVERT: A 1810 TYR cc_start: 0.7901 (m-80) cc_final: 0.7590 (m-80) outliers start: 35 outliers final: 27 residues processed: 195 average time/residue: 0.1032 time to fit residues: 29.4577 Evaluate side-chains 198 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1490 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1667 ARG Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141311 restraints weight = 21348.431| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.63 r_work: 0.3192 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 12040 Z= 0.168 Angle : 0.892 59.196 16293 Z= 0.487 Chirality : 0.043 0.409 1862 Planarity : 0.004 0.044 2028 Dihedral : 7.225 68.668 1670 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.57 % Allowed : 17.74 % Favored : 79.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1428 helix: 1.42 (0.18), residues: 790 sheet: -0.98 (0.61), residues: 70 loop : -2.66 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1133 TYR 0.016 0.001 TYR A1125 PHE 0.017 0.001 PHE A 583 TRP 0.017 0.001 TRP A 394 HIS 0.006 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (12031) covalent geometry : angle 0.88831 / 0.49 (16282) SS BOND : bond 0.00488 / 0.26 ( 1) SS BOND : angle 1.36852 / 0.73 ( 2) hydrogen bonds : bond 0.03365 / 2.08 ( 606) hydrogen bonds : angle 4.04408 / 2.68 ( 1764) metal coordination : bond 0.00809 / 0.42 ( 8) metal coordination : angle 3.52440 / 2.81 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 CYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7147 (m) REVERT: B 53 CYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7396 (m) REVERT: B 60 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7176 (t) REVERT: A 37 MET cc_start: 0.6148 (tpp) cc_final: 0.5882 (tpp) REVERT: A 420 ASN cc_start: 0.8687 (t0) cc_final: 0.8412 (t0) REVERT: A 456 TYR cc_start: 0.7616 (t80) cc_final: 0.7225 (t80) REVERT: A 647 MET cc_start: 0.8880 (tpt) cc_final: 0.8338 (tpt) REVERT: A 660 ASP cc_start: 0.8390 (t0) cc_final: 0.8129 (t0) REVERT: A 669 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7877 (p0) REVERT: A 694 MET cc_start: 0.8901 (tpt) cc_final: 0.8479 (tpt) REVERT: A 1150 GLU cc_start: 0.8377 (mp0) cc_final: 0.8065 (mp0) REVERT: A 1223 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6004 (mm) REVERT: A 1253 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7632 (mtmm) REVERT: A 1276 TYR cc_start: 0.8825 (m-10) cc_final: 0.8523 (m-10) REVERT: A 1311 GLU cc_start: 0.8057 (tp30) cc_final: 0.7559 (tp30) REVERT: A 1366 ASP cc_start: 0.8725 (t70) cc_final: 0.8232 (t0) REVERT: A 1368 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8049 (mt) REVERT: A 1467 ASP cc_start: 0.8181 (p0) cc_final: 0.7652 (p0) REVERT: A 1546 GLU cc_start: 0.7594 (pt0) cc_final: 0.7181 (pt0) REVERT: A 1667 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6695 (ptm160) REVERT: A 1810 TYR cc_start: 0.7855 (m-80) cc_final: 0.7541 (m-80) outliers start: 34 outliers final: 27 residues processed: 195 average time/residue: 0.1027 time to fit residues: 29.4809 Evaluate side-chains 197 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1490 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1667 ARG Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 0.0570 chunk 120 optimal weight: 8.9990 chunk 80 optimal weight: 0.0170 chunk 24 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 129 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 0.0070 chunk 132 optimal weight: 0.8980 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132216 restraints weight = 29133.233| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.10 r_work: 0.3193 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 12040 Z= 0.168 Angle : 0.892 59.196 16293 Z= 0.487 Chirality : 0.043 0.409 1862 Planarity : 0.004 0.044 2028 Dihedral : 7.225 68.668 1670 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.57 % Allowed : 17.74 % Favored : 79.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1428 helix: 1.42 (0.18), residues: 790 sheet: -0.98 (0.61), residues: 70 loop : -2.66 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1133 TYR 0.016 0.001 TYR A1125 PHE 0.017 0.001 PHE A 583 TRP 0.017 0.001 TRP A 394 HIS 0.006 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (12031) covalent geometry : angle 0.88831 / 0.49 (16282) SS BOND : bond 0.00488 / 0.26 ( 1) SS BOND : angle 1.36852 / 0.73 ( 2) hydrogen bonds : bond 0.03365 / 2.08 ( 606) hydrogen bonds : angle 4.04408 / 2.68 ( 1764) metal coordination : bond 0.00809 / 0.42 ( 8) metal coordination : angle 3.52440 / 2.81 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2948.89 seconds wall clock time: 51 minutes 39.12 seconds (3099.12 seconds total)