Starting phenix.real_space_refine on Tue May 5 15:49:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pe2_71551/05_2026/9pe2_71551_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pe2_71551/05_2026/9pe2_71551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pe2_71551/05_2026/9pe2_71551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pe2_71551/05_2026/9pe2_71551.map" model { file = "/net/cci-nas-00/data/ceres_data/9pe2_71551/05_2026/9pe2_71551_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pe2_71551/05_2026/9pe2_71551_trim.cif" } resolution = 3.07 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= 0.003 sd= 0.025 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 76 5.16 5 C 9784 2.51 5 N 2271 2.21 5 O 2541 1.98 5 H 13106 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27781 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 25607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1630, 25607 Classifications: {'peptide': 1630} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 1560} Chain breaks: 6 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 8, 'GLN:plan1': 5, 'TYR:plan': 1, 'ARG:plan': 12, 'ASN:plan1': 2, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 190 Chain: "G" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 960 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 57} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1119 Unusual residues: {'3PE': 1, 'NAG': 1, 'UDP': 1, 'Y01': 29} Classifications: {'undetermined': 32, 'water': 5} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.72, per 1000 atoms: 0.17 Number of scatterers: 27781 At special positions: 0 Unit cell: (94.92, 117.6, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 3 15.00 O 2541 8.00 N 2271 7.00 C 9784 6.00 H 13106 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1345 " 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 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-3 " BGC D 1 " - " BGC D 2 " " BGC D 2 " - " BGC D 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A2001 " - " ASN A1845 " " NAG B 1 " - " ASN A1849 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 770.7 milliseconds 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 3 sheets defined 69.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.604A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 200 removed outlier: 4.366A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.656A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 243 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.553A pdb=" N LEU A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.653A pdb=" N GLU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 321 through 338 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.532A pdb=" N GLN A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 357 through 369 removed outlier: 4.202A pdb=" N ILE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 removed outlier: 3.700A pdb=" N LEU A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 406 removed outlier: 3.647A pdb=" N ILE A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 418 through 426 removed outlier: 4.414A pdb=" N TYR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.592A pdb=" N TRP A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 518 removed outlier: 4.459A pdb=" N GLY A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 553 removed outlier: 4.167A pdb=" N ARG A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 555 through 583 removed outlier: 4.432A pdb=" N THR A 560 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 640 removed outlier: 3.736A pdb=" N TYR A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 671 through 712 removed outlier: 4.249A pdb=" N THR A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 764 removed outlier: 3.936A pdb=" N LEU A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 802 through 806 removed outlier: 3.617A pdb=" N THR A 806 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 828 Processing helix chain 'A' and resid 856 through 862 Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'A' and resid 880 through 898 Processing helix chain 'A' and resid 933 through 947 Processing helix chain 'A' and resid 949 through 972 removed outlier: 3.636A pdb=" N THR A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.918A pdb=" N VAL A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.724A pdb=" N LEU A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1080 through 1091 removed outlier: 4.375A pdb=" N ASP A1084 " --> pdb=" O ASP A1080 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE A1091 " --> pdb=" O ASN A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1113 Processing helix chain 'A' and resid 1114 through 1121 Processing helix chain 'A' and resid 1163 through 1188 removed outlier: 3.865A pdb=" N GLY A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A1180 " --> pdb=" O PHE A1176 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG A1182 " --> pdb=" O THR A1178 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1208 Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.996A pdb=" N TYR A1224 " --> pdb=" O ASN A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1272 removed outlier: 3.974A pdb=" N LEU A1271 " --> pdb=" O GLY A1267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A1272 " --> pdb=" O GLU A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1282 removed outlier: 3.590A pdb=" N TYR A1276 " --> pdb=" O SER A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1294 Processing helix chain 'A' and resid 1294 through 1325 removed outlier: 4.580A pdb=" N HIS A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A1313 " --> pdb=" O GLN A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1353 through 1369 removed outlier: 3.645A pdb=" N ARG A1357 " --> pdb=" O ASP A1353 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A1369 " --> pdb=" O VAL A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1381 Processing helix chain 'A' and resid 1382 through 1396 Processing helix chain 'A' and resid 1397 through 1419 removed outlier: 3.566A pdb=" N PHE A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1447 removed outlier: 4.833A pdb=" N GLY A1447 " --> pdb=" O SER A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1467 Processing helix chain 'A' and resid 1471 through 1490 removed outlier: 4.002A pdb=" N PHE A1475 " --> pdb=" O PRO A1471 " (cutoff:3.500A) Proline residue: A1486 - end of helix removed outlier: 3.641A pdb=" N ASN A1490 " --> pdb=" O PRO A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1512 removed outlier: 3.535A pdb=" N ASP A1505 " --> pdb=" O LEU A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1539 Processing helix chain 'A' and resid 1557 through 1584 removed outlier: 3.628A pdb=" N ILE A1561 " --> pdb=" O ARG A1557 " (cutoff:3.500A) Proline residue: A1567 - end of helix Processing helix chain 'A' and resid 1591 through 1595 Processing helix chain 'A' and resid 1597 through 1626 removed outlier: 3.881A pdb=" N ARG A1601 " --> pdb=" O ASN A1597 " (cutoff:3.500A) Proline residue: A1609 - end of helix Processing helix chain 'A' and resid 1637 through 1665 removed outlier: 3.837A pdb=" N VAL A1641 " --> pdb=" O LYS A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1696 removed outlier: 3.531A pdb=" N ILE A1674 " --> pdb=" O VAL A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1710 Processing helix chain 'A' and resid 1724 through 1754 removed outlier: 3.547A pdb=" N GLN A1754 " --> pdb=" O ILE A1750 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1760 removed outlier: 3.708A pdb=" N ILE A1760 " --> pdb=" O PRO A1756 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1773 removed outlier: 3.585A pdb=" N PHE A1766 " --> pdb=" O LYS A1762 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1825 Proline residue: A1818 - end of helix removed outlier: 3.935A pdb=" N ALA A1823 " --> pdb=" O ALA A1819 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A1824 " --> pdb=" O VAL A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1838 removed outlier: 4.032A pdb=" N VAL A1837 " --> pdb=" O ASP A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1857 removed outlier: 4.150A pdb=" N SER A1856 " --> pdb=" O GLY A1852 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 118 removed outlier: 3.801A pdb=" N THR G 108 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE G 109 " --> pdb=" O PRO G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 125 removed outlier: 4.230A pdb=" N ALA G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 removed outlier: 3.655A pdb=" N TYR G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 780 Processing sheet with id=AA3, first strand: chain 'A' and resid 1068 through 1072 removed outlier: 3.842A pdb=" N PHE A1068 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE A1047 " --> pdb=" O LEU A1072 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A1033 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR A 843 " --> pdb=" O GLN A1099 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A1149 " --> pdb=" O ASN A1200 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ARG A1235 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A1154 " --> pdb=" O CYS A1239 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR A1241 " --> pdb=" O ARG A1154 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N TYR A1156 " --> pdb=" O TYR A1241 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLN A1243 " --> pdb=" O TYR A1156 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N PHE A1158 " --> pdb=" O GLN A1243 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLY A1245 " --> pdb=" O PHE A1158 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2418 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: 6.04 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 0.99: 13066 0.99 - 1.19: 17 1.19 - 1.40: 6026 1.40 - 1.61: 8991 1.61 - 1.81: 129 Bond restraints: 28229 Sorted by residual: bond pdb=" C4' UDP A2032 " pdb=" C3' UDP A2032 " ideal model delta sigma weight residual 1.526 1.345 0.181 1.30e-02 5.92e+03 1.94e+02 bond pdb=" C4' UDP A2032 " pdb=" O4' UDP A2032 " ideal model delta sigma weight residual 1.444 1.608 -0.164 1.30e-02 5.92e+03 1.59e+02 bond pdb=" C5 UDP A2032 " pdb=" H5 UDP A2032 " ideal model delta sigma weight residual 0.930 1.085 -0.155 1.40e-02 5.10e+03 1.23e+02 bond pdb=" C6 UDP A2032 " pdb=" H6 UDP A2032 " ideal model delta sigma weight residual 0.930 1.084 -0.154 1.40e-02 5.10e+03 1.22e+02 bond pdb=" C1' UDP A2032 " pdb=" H1' UDP A2032 " ideal model delta sigma weight residual 0.970 1.086 -0.116 1.10e-02 8.26e+03 1.11e+02 ... (remaining 28224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 49650 3.23 - 6.46: 583 6.46 - 9.70: 104 9.70 - 12.93: 41 12.93 - 16.16: 10 Bond angle restraints: 50388 Sorted by residual: angle pdb=" C2 UDP A2032 " pdb=" N3 UDP A2032 " pdb=" C4 UDP A2032 " ideal model delta sigma weight residual 126.93 119.92 7.01 1.00e+00 1.00e+00 4.92e+01 angle pdb=" O2B UDP A2032 " pdb=" PB UDP A2032 " pdb=" O3A UDP A2032 " ideal model delta sigma weight residual 102.95 109.69 -6.74 1.00e+00 1.00e+00 4.54e+01 angle pdb=" O1B UDP A2032 " pdb=" PB UDP A2032 " pdb=" O3A UDP A2032 " ideal model delta sigma weight residual 102.95 109.42 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb="HD21 ASN A1849 " pdb=" ND2 ASN A1849 " pdb="HD22 ASN A1849 " ideal model delta sigma weight residual 120.00 103.84 16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" N3 UDP A2032 " pdb=" C4 UDP A2032 " pdb=" C5 UDP A2032 " ideal model delta sigma weight residual 114.70 119.94 -5.24 1.00e+00 1.00e+00 2.75e+01 ... (remaining 50383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.64: 14137 23.64 - 47.29: 697 47.29 - 70.93: 262 70.93 - 94.58: 19 94.58 - 118.22: 10 Dihedral angle restraints: 15125 sinusoidal: 8967 harmonic: 6158 Sorted by residual: dihedral pdb=" CA TRP G 122 " pdb=" C TRP G 122 " pdb=" N ALA G 123 " pdb=" CA ALA G 123 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR A1193 " pdb=" C TYR A1193 " pdb=" N GLY A1194 " pdb=" CA GLY A1194 " ideal model delta harmonic sigma weight residual 180.00 159.41 20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA VAL G 116 " pdb=" C VAL G 116 " pdb=" N SER G 117 " pdb=" CA SER G 117 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 15122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2102 0.095 - 0.189: 143 0.189 - 0.284: 37 0.284 - 0.379: 54 0.379 - 0.473: 29 Chirality restraints: 2365 Sorted by residual: chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.35e+01 chirality pdb=" C1 MAN B 4 " pdb=" O3 BMA B 3 " pdb=" C2 MAN B 4 " pdb=" O5 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.72e+01 chirality pdb=" C1 MAN B 5 " pdb=" O6 BMA B 3 " pdb=" C2 MAN B 5 " pdb=" O5 MAN B 5 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.54e+01 ... (remaining 2362 not shown) Planarity restraints: 4051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1849 " -0.106 2.00e-02 2.50e+03 3.99e-01 2.39e+03 pdb=" CG ASN A1849 " 0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN A1849 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN A1849 " 0.131 2.00e-02 2.50e+03 pdb="HD21 ASN A1849 " 0.597 2.00e-02 2.50e+03 pdb="HD22 ASN A1849 " -0.747 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 422 " 0.335 9.50e-02 1.11e+02 1.79e-01 4.52e+02 pdb=" NE ARG A 422 " 0.126 2.00e-02 2.50e+03 pdb=" CZ ARG A 422 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 422 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 422 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG A 422 " 0.263 2.00e-02 2.50e+03 pdb="HH12 ARG A 422 " -0.286 2.00e-02 2.50e+03 pdb="HH21 ARG A 422 " -0.061 2.00e-02 2.50e+03 pdb="HH22 ARG A 422 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1849 " 0.016 2.00e-02 2.50e+03 1.16e-01 2.03e+02 pdb=" CG ASN A1849 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A1849 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN A1849 " -0.239 2.00e-02 2.50e+03 pdb="HD21 ASN A1849 " 0.147 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.041 2.00e-02 2.50e+03 ... (remaining 4048 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 1448 2.20 - 2.80: 54816 2.80 - 3.40: 77361 3.40 - 4.00: 99952 4.00 - 4.60: 156151 Nonbonded interactions: 389728 Sorted by model distance: nonbonded pdb=" OG SER A 944 " pdb=" HG1 THR A 949 " model vdw 1.606 2.450 nonbonded pdb=" HH TYR A1451 " pdb=" OD1 ASP A1743 " model vdw 1.663 2.450 nonbonded pdb=" O ALA A1201 " pdb=" HG1 THR A1205 " model vdw 1.676 2.450 nonbonded pdb=" O GLN A 824 " pdb=" HG SER A 827 " model vdw 1.690 2.450 nonbonded pdb=" OE1 GLU A 883 " pdb=" HE ARG A 946 " model vdw 1.692 2.450 ... (remaining 389723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.270 Find NCS groups from input model: 0.180 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.008 0.181 15133 Z= 0.453 Angle : 1.248 20.518 20737 Z= 0.493 Chirality : 0.087 0.473 2365 Planarity : 0.006 0.100 2446 Dihedral : 15.505 118.222 7216 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.29 % Allowed : 3.93 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.03 (0.20), residues: 1679 helix: 2.21 (0.16), residues: 1025 sheet: 1.37 (0.63), residues: 61 loop : -0.17 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 356 TYR 0.010 0.001 TYR A1409 PHE 0.014 0.001 PHE A1363 TRP 0.012 0.001 TRP A 625 HIS 0.004 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00825 (15123) covalent geometry : angle 1.23822 (20709) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.36916 ( 4) hydrogen bonds : bond 0.13241 ( 820) hydrogen bonds : angle 5.48699 ( 2418) link_ALPHA1-3 : bond 0.00251 ( 1) link_ALPHA1-3 : angle 4.63662 ( 3) link_ALPHA1-6 : bond 0.00058 ( 1) link_ALPHA1-6 : angle 2.14842 ( 3) link_BETA1-3 : bond 0.00077 ( 2) link_BETA1-3 : angle 1.22178 ( 6) link_BETA1-4 : bond 0.00744 ( 2) link_BETA1-4 : angle 2.25558 ( 6) link_NAG-ASN : bond 0.07714 ( 2) link_NAG-ASN : angle 8.44726 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8876 (mmp) cc_final: 0.8537 (mmp) REVERT: A 338 SER cc_start: 0.9194 (t) cc_final: 0.8909 (p) REVERT: A 664 TRP cc_start: 0.7019 (m-10) cc_final: 0.6691 (m-10) REVERT: A 691 ASP cc_start: 0.8411 (t0) cc_final: 0.8208 (t0) REVERT: A 745 LYS cc_start: 0.8402 (mttt) cc_final: 0.8122 (mtpt) REVERT: A 816 GLU cc_start: 0.7885 (tt0) cc_final: 0.7681 (tt0) REVERT: A 885 GLU cc_start: 0.9050 (tt0) cc_final: 0.8825 (tt0) REVERT: A 935 TYR cc_start: 0.7859 (m-80) cc_final: 0.7375 (t80) REVERT: A 1128 GLU cc_start: 0.8562 (tt0) cc_final: 0.8350 (pm20) REVERT: A 1224 TYR cc_start: 0.8752 (m-80) cc_final: 0.8010 (m-80) REVERT: A 1384 TRP cc_start: 0.7545 (m100) cc_final: 0.6555 (t-100) REVERT: A 1661 MET cc_start: 0.9327 (tpp) cc_final: 0.9011 (tpp) outliers start: 4 outliers final: 3 residues processed: 215 average time/residue: 0.3041 time to fit residues: 91.8662 Evaluate side-chains 140 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1133 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 453 ASN A 542 ASN A 752 GLN A 982 ASN A1107 ASN A1142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.075570 restraints weight = 64828.455| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.18 r_work: 0.2871 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15133 Z= 0.130 Angle : 0.586 6.852 20737 Z= 0.284 Chirality : 0.039 0.346 2365 Planarity : 0.004 0.046 2446 Dihedral : 12.336 101.562 4179 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.07 % Allowed : 7.22 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.17 (0.20), residues: 1679 helix: 2.25 (0.16), residues: 1049 sheet: 1.38 (0.64), residues: 61 loop : -0.07 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 134 TYR 0.011 0.001 TYR A 968 PHE 0.016 0.001 PHE A1203 TRP 0.011 0.001 TRP A 625 HIS 0.004 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00268 (15123) covalent geometry : angle 0.58045 (20709) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.38136 ( 4) hydrogen bonds : bond 0.05606 ( 820) hydrogen bonds : angle 4.65400 ( 2418) link_ALPHA1-3 : bond 0.00160 ( 1) link_ALPHA1-3 : angle 4.27188 ( 3) link_ALPHA1-6 : bond 0.00233 ( 1) link_ALPHA1-6 : angle 1.89934 ( 3) link_BETA1-3 : bond 0.00277 ( 2) link_BETA1-3 : angle 2.21566 ( 6) link_BETA1-4 : bond 0.00915 ( 2) link_BETA1-4 : angle 1.96364 ( 6) link_NAG-ASN : bond 0.00506 ( 2) link_NAG-ASN : angle 2.16134 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8885 (mmp) cc_final: 0.8598 (mmp) REVERT: A 338 SER cc_start: 0.9202 (t) cc_final: 0.8834 (p) REVERT: A 619 TRP cc_start: 0.7418 (m100) cc_final: 0.6584 (m100) REVERT: A 745 LYS cc_start: 0.8355 (mttt) cc_final: 0.8075 (mtpt) REVERT: A 816 GLU cc_start: 0.8065 (tt0) cc_final: 0.7836 (tt0) REVERT: A 885 GLU cc_start: 0.9179 (tt0) cc_final: 0.8967 (tt0) REVERT: A 935 TYR cc_start: 0.7839 (m-80) cc_final: 0.7251 (t80) REVERT: A 958 MET cc_start: 0.8764 (mmm) cc_final: 0.8307 (tpt) REVERT: A 1128 GLU cc_start: 0.8684 (tt0) cc_final: 0.8376 (pm20) REVERT: A 1224 TYR cc_start: 0.8694 (m-80) cc_final: 0.8059 (m-80) REVERT: A 1380 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8127 (mt-10) outliers start: 15 outliers final: 9 residues processed: 157 average time/residue: 0.3028 time to fit residues: 67.3556 Evaluate side-chains 137 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1616 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 130 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1583 ASN ** A1748 HIS ** 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 = 0.3382 r_free = 0.3382 target = 0.105355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.071778 restraints weight = 65459.928| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.93 r_work: 0.2684 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15133 Z= 0.258 Angle : 0.619 7.163 20737 Z= 0.311 Chirality : 0.041 0.264 2365 Planarity : 0.004 0.046 2446 Dihedral : 11.289 87.433 4179 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.14 % Allowed : 8.73 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.92 (0.20), residues: 1679 helix: 2.14 (0.16), residues: 1041 sheet: 0.83 (0.63), residues: 61 loop : -0.28 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1444 TYR 0.015 0.001 TYR A1804 PHE 0.016 0.002 PHE A1657 TRP 0.014 0.001 TRP A 625 HIS 0.005 0.001 HIS A1298 Details of bonding type rmsd covalent geometry : bond 0.00581 (15123) covalent geometry : angle 0.61446 (20709) SS BOND : bond 0.00555 ( 2) SS BOND : angle 0.93599 ( 4) hydrogen bonds : bond 0.05752 ( 820) hydrogen bonds : angle 4.61661 ( 2418) link_ALPHA1-3 : bond 0.00208 ( 1) link_ALPHA1-3 : angle 3.56082 ( 3) link_ALPHA1-6 : bond 0.00330 ( 1) link_ALPHA1-6 : angle 2.09742 ( 3) link_BETA1-3 : bond 0.00326 ( 2) link_BETA1-3 : angle 2.45728 ( 6) link_BETA1-4 : bond 0.00396 ( 2) link_BETA1-4 : angle 1.81242 ( 6) link_NAG-ASN : bond 0.00262 ( 2) link_NAG-ASN : angle 1.39618 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8621 (mmp) cc_final: 0.8353 (mmp) REVERT: A 338 SER cc_start: 0.9069 (t) cc_final: 0.8621 (p) REVERT: A 619 TRP cc_start: 0.7197 (m100) cc_final: 0.6363 (m100) REVERT: A 745 LYS cc_start: 0.8201 (mttt) cc_final: 0.7945 (mtpt) REVERT: A 816 GLU cc_start: 0.8028 (tt0) cc_final: 0.7802 (tt0) REVERT: A 935 TYR cc_start: 0.7798 (m-80) cc_final: 0.7183 (t80) REVERT: A 993 MET cc_start: 0.8236 (tpp) cc_final: 0.7960 (tpp) REVERT: A 1128 GLU cc_start: 0.8730 (tt0) cc_final: 0.8288 (pm20) REVERT: A 1661 MET cc_start: 0.8992 (tpp) cc_final: 0.8564 (tpp) outliers start: 16 outliers final: 11 residues processed: 147 average time/residue: 0.3142 time to fit residues: 65.5490 Evaluate side-chains 133 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1480 SER Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1521 SER Chi-restraints excluded: chain A residue 1529 SER Chi-restraints excluded: chain A residue 1616 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 141 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1269 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.073838 restraints weight = 64443.341| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.94 r_work: 0.2833 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15133 Z= 0.129 Angle : 0.532 8.100 20737 Z= 0.263 Chirality : 0.037 0.299 2365 Planarity : 0.004 0.045 2446 Dihedral : 10.494 71.455 4177 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.79 % Allowed : 10.23 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.15 (0.20), residues: 1679 helix: 2.33 (0.16), residues: 1041 sheet: 0.77 (0.63), residues: 61 loop : -0.17 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 134 TYR 0.011 0.001 TYR A1291 PHE 0.013 0.001 PHE A1657 TRP 0.012 0.001 TRP A 625 HIS 0.003 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00279 (15123) covalent geometry : angle 0.52701 (20709) SS BOND : bond 0.00349 ( 2) SS BOND : angle 0.61198 ( 4) hydrogen bonds : bond 0.04953 ( 820) hydrogen bonds : angle 4.35290 ( 2418) link_ALPHA1-3 : bond 0.00025 ( 1) link_ALPHA1-3 : angle 3.92227 ( 3) link_ALPHA1-6 : bond 0.00717 ( 1) link_ALPHA1-6 : angle 2.37654 ( 3) link_BETA1-3 : bond 0.00212 ( 2) link_BETA1-3 : angle 2.36551 ( 6) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 1.57950 ( 6) link_NAG-ASN : bond 0.00313 ( 2) link_NAG-ASN : angle 1.18913 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8876 (mmp) cc_final: 0.8419 (mmp) REVERT: A 338 SER cc_start: 0.9227 (t) cc_final: 0.8889 (p) REVERT: A 619 TRP cc_start: 0.7442 (m100) cc_final: 0.6589 (m100) REVERT: A 691 ASP cc_start: 0.8290 (t70) cc_final: 0.8002 (t0) REVERT: A 745 LYS cc_start: 0.8290 (mttt) cc_final: 0.8025 (mtpt) REVERT: A 816 GLU cc_start: 0.8121 (tt0) cc_final: 0.7887 (tt0) REVERT: A 935 TYR cc_start: 0.7856 (m-80) cc_final: 0.7263 (t80) REVERT: A 993 MET cc_start: 0.8573 (tpp) cc_final: 0.8327 (tpp) REVERT: A 1128 GLU cc_start: 0.8729 (tt0) cc_final: 0.8391 (pm20) REVERT: A 1224 TYR cc_start: 0.8800 (m-80) cc_final: 0.8173 (m-80) REVERT: A 1661 MET cc_start: 0.9234 (tpp) cc_final: 0.8861 (tpp) outliers start: 11 outliers final: 9 residues processed: 140 average time/residue: 0.2912 time to fit residues: 57.9312 Evaluate side-chains 133 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1529 SER Chi-restraints excluded: chain A residue 1616 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 149 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 GLN A1269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.071455 restraints weight = 65380.516| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.17 r_work: 0.2796 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15133 Z= 0.175 Angle : 0.543 8.396 20737 Z= 0.269 Chirality : 0.038 0.295 2365 Planarity : 0.004 0.052 2446 Dihedral : 9.779 59.960 4177 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.00 % Allowed : 10.52 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.16 (0.21), residues: 1679 helix: 2.37 (0.16), residues: 1041 sheet: 0.48 (0.63), residues: 61 loop : -0.21 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 134 TYR 0.012 0.001 TYR A1804 PHE 0.016 0.001 PHE A1500 TRP 0.014 0.001 TRP A 664 HIS 0.002 0.001 HIS A1238 Details of bonding type rmsd covalent geometry : bond 0.00394 (15123) covalent geometry : angle 0.53803 (20709) SS BOND : bond 0.00383 ( 2) SS BOND : angle 0.61193 ( 4) hydrogen bonds : bond 0.04922 ( 820) hydrogen bonds : angle 4.32421 ( 2418) link_ALPHA1-3 : bond 0.00159 ( 1) link_ALPHA1-3 : angle 3.76891 ( 3) link_ALPHA1-6 : bond 0.00654 ( 1) link_ALPHA1-6 : angle 1.63165 ( 3) link_BETA1-3 : bond 0.00253 ( 2) link_BETA1-3 : angle 2.31894 ( 6) link_BETA1-4 : bond 0.00500 ( 2) link_BETA1-4 : angle 1.80325 ( 6) link_NAG-ASN : bond 0.00335 ( 2) link_NAG-ASN : angle 1.17439 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 SER cc_start: 0.9226 (t) cc_final: 0.8869 (p) REVERT: A 619 TRP cc_start: 0.7473 (m100) cc_final: 0.6594 (m100) REVERT: A 742 ILE cc_start: 0.6045 (tp) cc_final: 0.5824 (tt) REVERT: A 745 LYS cc_start: 0.8235 (mttt) cc_final: 0.7961 (mtpt) REVERT: A 816 GLU cc_start: 0.8138 (tt0) cc_final: 0.7918 (tt0) REVERT: A 935 TYR cc_start: 0.7853 (m-80) cc_final: 0.7250 (t80) REVERT: A 993 MET cc_start: 0.8543 (tpp) cc_final: 0.8299 (tpp) REVERT: A 1128 GLU cc_start: 0.8771 (tt0) cc_final: 0.8374 (pm20) REVERT: A 1661 MET cc_start: 0.9208 (tpp) cc_final: 0.8831 (tpp) outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 0.3079 time to fit residues: 61.4519 Evaluate side-chains 135 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1529 SER Chi-restraints excluded: chain A residue 1616 VAL Chi-restraints excluded: chain A residue 1693 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 131 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1514 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.075899 restraints weight = 63822.092| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.91 r_work: 0.2791 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15133 Z= 0.159 Angle : 0.525 7.534 20737 Z= 0.261 Chirality : 0.037 0.261 2365 Planarity : 0.004 0.054 2446 Dihedral : 9.306 58.864 4177 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.07 % Allowed : 10.44 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.19 (0.21), residues: 1679 helix: 2.45 (0.16), residues: 1032 sheet: 0.26 (0.63), residues: 61 loop : -0.24 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 134 TYR 0.012 0.001 TYR A1804 PHE 0.019 0.001 PHE G 112 TRP 0.015 0.001 TRP A 664 HIS 0.005 0.001 HIS A1298 Details of bonding type rmsd covalent geometry : bond 0.00356 (15123) covalent geometry : angle 0.52070 (20709) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.62367 ( 4) hydrogen bonds : bond 0.04787 ( 820) hydrogen bonds : angle 4.25873 ( 2418) link_ALPHA1-3 : bond 0.00210 ( 1) link_ALPHA1-3 : angle 3.55687 ( 3) link_ALPHA1-6 : bond 0.00482 ( 1) link_ALPHA1-6 : angle 1.56281 ( 3) link_BETA1-3 : bond 0.00244 ( 2) link_BETA1-3 : angle 2.31070 ( 6) link_BETA1-4 : bond 0.00306 ( 2) link_BETA1-4 : angle 1.77727 ( 6) link_NAG-ASN : bond 0.00276 ( 2) link_NAG-ASN : angle 1.06350 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8672 (mmp) cc_final: 0.8275 (mmp) REVERT: A 338 SER cc_start: 0.9114 (t) cc_final: 0.8751 (p) REVERT: A 656 MET cc_start: 0.9183 (mmm) cc_final: 0.8907 (mmm) REVERT: A 745 LYS cc_start: 0.8147 (mttt) cc_final: 0.7863 (mtpt) REVERT: A 935 TYR cc_start: 0.7812 (m-80) cc_final: 0.7192 (t80) REVERT: A 993 MET cc_start: 0.8354 (tpp) cc_final: 0.8135 (tpp) REVERT: A 1128 GLU cc_start: 0.8788 (tt0) cc_final: 0.8318 (pm20) REVERT: A 1224 TYR cc_start: 0.8624 (m-80) cc_final: 0.8019 (m-80) REVERT: A 1661 MET cc_start: 0.9049 (tpp) cc_final: 0.8705 (tpp) outliers start: 15 outliers final: 10 residues processed: 141 average time/residue: 0.3130 time to fit residues: 62.6564 Evaluate side-chains 132 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1529 SER Chi-restraints excluded: chain A residue 1616 VAL Chi-restraints excluded: chain A residue 1693 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1269 GLN ** A1748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.074566 restraints weight = 64242.774| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.92 r_work: 0.2767 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15133 Z= 0.220 Angle : 0.554 6.624 20737 Z= 0.277 Chirality : 0.039 0.249 2365 Planarity : 0.004 0.057 2446 Dihedral : 9.237 59.361 4177 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.00 % Allowed : 10.44 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.13 (0.21), residues: 1679 helix: 2.42 (0.16), residues: 1032 sheet: 0.24 (0.64), residues: 61 loop : -0.29 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 134 TYR 0.014 0.001 TYR A1804 PHE 0.016 0.001 PHE A1657 TRP 0.013 0.001 TRP A 664 HIS 0.003 0.001 HIS A1238 Details of bonding type rmsd covalent geometry : bond 0.00501 (15123) covalent geometry : angle 0.54984 (20709) SS BOND : bond 0.00448 ( 2) SS BOND : angle 0.68062 ( 4) hydrogen bonds : bond 0.04974 ( 820) hydrogen bonds : angle 4.31647 ( 2418) link_ALPHA1-3 : bond 0.00186 ( 1) link_ALPHA1-3 : angle 3.49405 ( 3) link_ALPHA1-6 : bond 0.00510 ( 1) link_ALPHA1-6 : angle 1.50488 ( 3) link_BETA1-3 : bond 0.00263 ( 2) link_BETA1-3 : angle 2.31349 ( 6) link_BETA1-4 : bond 0.00324 ( 2) link_BETA1-4 : angle 1.78088 ( 6) link_NAG-ASN : bond 0.00251 ( 2) link_NAG-ASN : angle 1.18077 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 SER cc_start: 0.9130 (t) cc_final: 0.8761 (p) REVERT: A 935 TYR cc_start: 0.7863 (m-80) cc_final: 0.7276 (t80) REVERT: A 993 MET cc_start: 0.8345 (tpp) cc_final: 0.8131 (tpp) REVERT: A 1128 GLU cc_start: 0.8798 (tt0) cc_final: 0.8357 (pm20) REVERT: A 1661 MET cc_start: 0.9050 (tpp) cc_final: 0.8689 (tpp) outliers start: 14 outliers final: 10 residues processed: 138 average time/residue: 0.3128 time to fit residues: 60.5384 Evaluate side-chains 135 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1425 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1529 SER Chi-restraints excluded: chain A residue 1616 VAL Chi-restraints excluded: chain A residue 1693 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 47 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 155 optimal weight: 0.0040 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1269 GLN ** A1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.076321 restraints weight = 63662.330| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.91 r_work: 0.2796 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15133 Z= 0.131 Angle : 0.514 7.756 20737 Z= 0.256 Chirality : 0.037 0.243 2365 Planarity : 0.004 0.066 2446 Dihedral : 8.927 59.922 4177 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.57 % Allowed : 11.23 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.29 (0.21), residues: 1679 helix: 2.54 (0.16), residues: 1032 sheet: 0.24 (0.65), residues: 61 loop : -0.22 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 134 TYR 0.010 0.001 TYR A1804 PHE 0.015 0.001 PHE A1657 TRP 0.012 0.001 TRP A 625 HIS 0.003 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00291 (15123) covalent geometry : angle 0.50944 (20709) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.37226 ( 4) hydrogen bonds : bond 0.04579 ( 820) hydrogen bonds : angle 4.18170 ( 2418) link_ALPHA1-3 : bond 0.00248 ( 1) link_ALPHA1-3 : angle 3.44147 ( 3) link_ALPHA1-6 : bond 0.00397 ( 1) link_ALPHA1-6 : angle 1.45066 ( 3) link_BETA1-3 : bond 0.00222 ( 2) link_BETA1-3 : angle 2.29820 ( 6) link_BETA1-4 : bond 0.00289 ( 2) link_BETA1-4 : angle 1.74935 ( 6) link_NAG-ASN : bond 0.00292 ( 2) link_NAG-ASN : angle 1.08494 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 SER cc_start: 0.9130 (t) cc_final: 0.8765 (p) REVERT: A 691 ASP cc_start: 0.8226 (t70) cc_final: 0.7901 (t0) REVERT: A 935 TYR cc_start: 0.7816 (m-80) cc_final: 0.7233 (t80) REVERT: A 993 MET cc_start: 0.8361 (tpp) cc_final: 0.8159 (tpp) REVERT: A 1128 GLU cc_start: 0.8792 (tt0) cc_final: 0.8324 (pm20) REVERT: A 1224 TYR cc_start: 0.8616 (m-80) cc_final: 0.7996 (m-80) REVERT: A 1380 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 1619 PHE cc_start: 0.8233 (m-80) cc_final: 0.8008 (t80) REVERT: A 1661 MET cc_start: 0.9039 (tpp) cc_final: 0.8716 (tpp) outliers start: 8 outliers final: 8 residues processed: 135 average time/residue: 0.3104 time to fit residues: 59.3056 Evaluate side-chains 132 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1425 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1529 SER Chi-restraints excluded: chain A residue 1616 VAL Chi-restraints excluded: chain A residue 1693 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 22 optimal weight: 0.0370 chunk 162 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1269 GLN ** A1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.074677 restraints weight = 64103.881| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.94 r_work: 0.2766 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15133 Z= 0.191 Angle : 0.536 6.036 20737 Z= 0.269 Chirality : 0.038 0.223 2365 Planarity : 0.004 0.066 2446 Dihedral : 8.926 59.793 4177 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.86 % Allowed : 10.73 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.24 (0.21), residues: 1679 helix: 2.51 (0.16), residues: 1032 sheet: 0.15 (0.65), residues: 61 loop : -0.25 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 134 TYR 0.014 0.001 TYR A1804 PHE 0.016 0.001 PHE A1657 TRP 0.016 0.001 TRP A 664 HIS 0.004 0.001 HIS A1298 Details of bonding type rmsd covalent geometry : bond 0.00435 (15123) covalent geometry : angle 0.53222 (20709) SS BOND : bond 0.00497 ( 2) SS BOND : angle 0.51243 ( 4) hydrogen bonds : bond 0.04814 ( 820) hydrogen bonds : angle 4.24503 ( 2418) link_ALPHA1-3 : bond 0.00291 ( 1) link_ALPHA1-3 : angle 3.21963 ( 3) link_ALPHA1-6 : bond 0.00322 ( 1) link_ALPHA1-6 : angle 1.56510 ( 3) link_BETA1-3 : bond 0.00248 ( 2) link_BETA1-3 : angle 2.29283 ( 6) link_BETA1-4 : bond 0.00280 ( 2) link_BETA1-4 : angle 1.87200 ( 6) link_NAG-ASN : bond 0.00212 ( 2) link_NAG-ASN : angle 1.19287 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 SER cc_start: 0.9153 (t) cc_final: 0.8784 (p) REVERT: A 656 MET cc_start: 0.9181 (mmm) cc_final: 0.8912 (mmm) REVERT: A 809 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8762 (m-80) REVERT: A 935 TYR cc_start: 0.7893 (m-80) cc_final: 0.7267 (t80) REVERT: A 993 MET cc_start: 0.8348 (tpp) cc_final: 0.8145 (tpp) REVERT: A 1128 GLU cc_start: 0.8804 (tt0) cc_final: 0.8357 (pm20) REVERT: A 1384 TRP cc_start: 0.7627 (m100) cc_final: 0.6481 (t-100) REVERT: A 1619 PHE cc_start: 0.8279 (m-80) cc_final: 0.8027 (t80) REVERT: A 1661 MET cc_start: 0.9053 (tpp) cc_final: 0.8702 (tpp) outliers start: 12 outliers final: 11 residues processed: 133 average time/residue: 0.3140 time to fit residues: 59.2030 Evaluate side-chains 136 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1425 ILE Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1529 SER Chi-restraints excluded: chain A residue 1616 VAL Chi-restraints excluded: chain A residue 1693 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1269 GLN ** A1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.075520 restraints weight = 63805.154| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.95 r_work: 0.2780 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15133 Z= 0.152 Angle : 0.512 5.752 20737 Z= 0.256 Chirality : 0.037 0.212 2365 Planarity : 0.004 0.069 2446 Dihedral : 8.771 59.853 4177 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.72 % Allowed : 10.80 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.31 (0.21), residues: 1679 helix: 2.56 (0.16), residues: 1034 sheet: 0.19 (0.65), residues: 61 loop : -0.20 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 134 TYR 0.012 0.001 TYR A1804 PHE 0.015 0.001 PHE A1657 TRP 0.013 0.001 TRP A 664 HIS 0.003 0.001 HIS A1298 Details of bonding type rmsd covalent geometry : bond 0.00341 (15123) covalent geometry : angle 0.50745 (20709) SS BOND : bond 0.00377 ( 2) SS BOND : angle 0.46113 ( 4) hydrogen bonds : bond 0.04613 ( 820) hydrogen bonds : angle 4.17511 ( 2418) link_ALPHA1-3 : bond 0.00293 ( 1) link_ALPHA1-3 : angle 3.09645 ( 3) link_ALPHA1-6 : bond 0.00353 ( 1) link_ALPHA1-6 : angle 1.51331 ( 3) link_BETA1-3 : bond 0.00246 ( 2) link_BETA1-3 : angle 2.27440 ( 6) link_BETA1-4 : bond 0.00271 ( 2) link_BETA1-4 : angle 1.83471 ( 6) link_NAG-ASN : bond 0.00251 ( 2) link_NAG-ASN : angle 1.08380 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 139 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue VAL 483 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue SER 798 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue THR 898 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue THR 1427 is missing expected H atoms. Skipping. Residue LYS 1537 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue LYS 1636 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1710 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 SER cc_start: 0.9154 (t) cc_final: 0.8791 (p) REVERT: A 809 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: A 935 TYR cc_start: 0.7853 (m-80) cc_final: 0.7214 (t80) REVERT: A 1128 GLU cc_start: 0.8807 (tt0) cc_final: 0.8321 (pm20) REVERT: A 1294 HIS cc_start: 0.8513 (t70) cc_final: 0.8148 (t70) REVERT: A 1384 TRP cc_start: 0.7615 (m100) cc_final: 0.6467 (t-100) REVERT: A 1619 PHE cc_start: 0.8296 (m-80) cc_final: 0.8061 (t80) REVERT: A 1661 MET cc_start: 0.9072 (tpp) cc_final: 0.8747 (tpp) outliers start: 10 outliers final: 9 residues processed: 133 average time/residue: 0.2974 time to fit residues: 56.8434 Evaluate side-chains 134 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1425 ILE Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1529 SER Chi-restraints excluded: chain A residue 1616 VAL Chi-restraints excluded: chain A residue 1693 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 36 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1269 GLN ** A1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075287 restraints weight = 63913.527| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.92 r_work: 0.2784 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15133 Z= 0.164 Angle : 0.513 5.398 20737 Z= 0.258 Chirality : 0.037 0.188 2365 Planarity : 0.004 0.068 2446 Dihedral : 8.678 59.782 4177 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.07 % Allowed : 10.52 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 2.30 (0.21), residues: 1679 helix: 2.58 (0.16), residues: 1035 sheet: -0.09 (0.65), residues: 63 loop : -0.23 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 134 TYR 0.012 0.001 TYR A1804 PHE 0.016 0.001 PHE A1657 TRP 0.015 0.001 TRP A 664 HIS 0.003 0.001 HIS A1298 Details of bonding type rmsd covalent geometry : bond 0.00371 (15123) covalent geometry : angle 0.50857 (20709) SS BOND : bond 0.00389 ( 2) SS BOND : angle 0.47724 ( 4) hydrogen bonds : bond 0.04624 ( 820) hydrogen bonds : angle 4.17336 ( 2418) link_ALPHA1-3 : bond 0.00309 ( 1) link_ALPHA1-3 : angle 2.84555 ( 3) link_ALPHA1-6 : bond 0.00269 ( 1) link_ALPHA1-6 : angle 1.58329 ( 3) link_BETA1-3 : bond 0.00238 ( 2) link_BETA1-3 : angle 2.23621 ( 6) link_BETA1-4 : bond 0.00270 ( 2) link_BETA1-4 : angle 1.91932 ( 6) link_NAG-ASN : bond 0.00221 ( 2) link_NAG-ASN : angle 1.10136 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5113.66 seconds wall clock time: 87 minutes 27.65 seconds (5247.65 seconds total)