Starting phenix.real_space_refine on Tue Aug 26 10:16:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gzn_34399/08_2025/8gzn_34399.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzn_34399/08_2025/8gzn_34399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gzn_34399/08_2025/8gzn_34399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzn_34399/08_2025/8gzn_34399.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gzn_34399/08_2025/8gzn_34399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzn_34399/08_2025/8gzn_34399.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 217 5.16 5 C 22277 2.51 5 N 6013 2.21 5 O 6815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35322 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 119} Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain: "C" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain breaks: 1 Chain: "G" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1785 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain breaks: 1 Chain: "I" Number of atoms: 9208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 9208 Classifications: {'peptide': 1115} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 1088} Chain breaks: 13 Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "K" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain breaks: 1 Chain: "L" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 114} Chain breaks: 1 Chain: "M" Number of atoms: 9208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 9208 Classifications: {'peptide': 1115} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 1088} Chain breaks: 13 Time building chain proxies: 8.38, per 1000 atoms: 0.24 Number of scatterers: 35322 At special positions: 0 Unit cell: (191.4, 174.9, 188.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 217 16.00 O 6815 8.00 N 6013 7.00 C 22277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.04 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.04 Simple disulfide: pdb=" SG CYS H 575 " - pdb=" SG CYS K 575 " distance=2.03 Simple disulfide: pdb=" SG CYS I 975 " - pdb=" SG CYS I1099 " distance=2.03 Simple disulfide: pdb=" SG CYS I 987 " - pdb=" SG CYS I1005 " distance=2.03 Simple disulfide: pdb=" SG CYS I1219 " - pdb=" SG CYS I1418 " distance=2.03 Simple disulfide: pdb=" SG CYS I1230 " - pdb=" SG CYS I1273 " distance=2.03 Simple disulfide: pdb=" SG CYS I1344 " - pdb=" SG CYS I1437 " distance=2.03 Simple disulfide: pdb=" SG CYS I1462 " - pdb=" SG CYS I1546 " distance=2.03 Simple disulfide: pdb=" SG CYS I1476 " - pdb=" SG CYS I1501 " distance=2.03 Simple disulfide: pdb=" SG CYS I1486 " - pdb=" SG CYS I1576 " distance=2.03 Simple disulfide: pdb=" SG CYS I1505 " - pdb=" SG CYS I1574 " distance=2.04 Simple disulfide: pdb=" SG CYS I1596 " - pdb=" SG CYS I1632 " distance=2.03 Simple disulfide: pdb=" SG CYS I1688 " - pdb=" SG CYS I1782 " distance=2.03 Simple disulfide: pdb=" SG CYS I1689 " - pdb=" SG CYS I1906 " distance=2.03 Simple disulfide: pdb=" SG CYS I1807 " - pdb=" SG CYS I1909 " distance=2.03 Simple disulfide: pdb=" SG CYS I1821 " - pdb=" SG CYS I1838 " distance=2.03 Simple disulfide: pdb=" SG CYS I1842 " - pdb=" SG CYS I1961 " distance=2.03 Simple disulfide: pdb=" SG CYS I1896 " - pdb=" SG CYS I1907 " distance=2.03 Simple disulfide: pdb=" SG CYS I2012 " - pdb=" SG CYS I2049 " distance=2.03 Simple disulfide: pdb=" SG CYS I2210 " - pdb=" SG CYS I2226 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.04 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Simple disulfide: pdb=" SG CYS M 975 " - pdb=" SG CYS M1099 " distance=2.03 Simple disulfide: pdb=" SG CYS M 987 " - pdb=" SG CYS M1005 " distance=2.03 Simple disulfide: pdb=" SG CYS M1219 " - pdb=" SG CYS M1418 " distance=2.03 Simple disulfide: pdb=" SG CYS M1230 " - pdb=" SG CYS M1273 " distance=2.03 Simple disulfide: pdb=" SG CYS M1251 " - pdb=" SG CYS M1264 " distance=2.03 Simple disulfide: pdb=" SG CYS M1344 " - pdb=" SG CYS M1437 " distance=2.03 Simple disulfide: pdb=" SG CYS M1462 " - pdb=" SG CYS M1546 " distance=2.03 Simple disulfide: pdb=" SG CYS M1476 " - pdb=" SG CYS M1501 " distance=2.03 Simple disulfide: pdb=" SG CYS M1486 " - pdb=" SG CYS M1576 " distance=2.03 Simple disulfide: pdb=" SG CYS M1505 " - pdb=" SG CYS M1574 " distance=2.03 Simple disulfide: pdb=" SG CYS M1596 " - pdb=" SG CYS M1632 " distance=2.03 Simple disulfide: pdb=" SG CYS M1688 " - pdb=" SG CYS M1782 " distance=2.03 Simple disulfide: pdb=" SG CYS M1689 " - pdb=" SG CYS M1906 " distance=2.03 Simple disulfide: pdb=" SG CYS M1807 " - pdb=" SG CYS M1909 " distance=2.03 Simple disulfide: pdb=" SG CYS M1821 " - pdb=" SG CYS M1838 " distance=2.03 Simple disulfide: pdb=" SG CYS M1842 " - pdb=" SG CYS M1961 " distance=2.03 Simple disulfide: pdb=" SG CYS M1896 " - pdb=" SG CYS M1907 " distance=2.03 Simple disulfide: pdb=" SG CYS M2012 " - pdb=" SG CYS M2049 " distance=2.03 Simple disulfide: pdb=" SG CYS M2210 " - pdb=" SG CYS M2226 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 8616 Ramachandran restraints generated. 4308 Oldfield, 0 Emsley, 4308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8378 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 52 sheets defined 35.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.636A pdb=" N TRP A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 421 removed outlier: 4.217A pdb=" N GLY C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 420 removed outlier: 3.651A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 467 Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'D' and resid 525 through 531 Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 414 through 420 removed outlier: 3.748A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 530 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 420 removed outlier: 4.332A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 466 removed outlier: 3.724A pdb=" N LEU F 466 " --> pdb=" O GLN F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 524 through 529 Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 414 through 420 Processing helix chain 'G' and resid 462 through 467 removed outlier: 3.857A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG G 467 " --> pdb=" O GLN G 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 462 through 467' Processing helix chain 'G' and resid 526 through 530 removed outlier: 3.587A pdb=" N THR G 530 " --> pdb=" O GLU G 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 420 Processing helix chain 'H' and resid 496 through 498 No H-bonds generated for 'chain 'H' and resid 496 through 498' Processing helix chain 'H' and resid 525 through 530 removed outlier: 3.948A pdb=" N ASN H 529 " --> pdb=" O GLU H 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 977 removed outlier: 3.799A pdb=" N ASP I 977 " --> pdb=" O GLU I 973 " (cutoff:3.500A) Processing helix chain 'I' and resid 1026 through 1051 removed outlier: 4.317A pdb=" N THR I1030 " --> pdb=" O GLY I1026 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN I1037 " --> pdb=" O ASN I1033 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN I1048 " --> pdb=" O TYR I1044 " (cutoff:3.500A) Processing helix chain 'I' and resid 1094 through 1125 Processing helix chain 'I' and resid 1142 through 1157 removed outlier: 3.782A pdb=" N TYR I1153 " --> pdb=" O CYS I1149 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR I1157 " --> pdb=" O TYR I1153 " (cutoff:3.500A) Processing helix chain 'I' and resid 1172 through 1180 Processing helix chain 'I' and resid 1189 through 1200 removed outlier: 3.532A pdb=" N LYS I1196 " --> pdb=" O SER I1192 " (cutoff:3.500A) Processing helix chain 'I' and resid 1266 through 1271 Processing helix chain 'I' and resid 1274 through 1276 No H-bonds generated for 'chain 'I' and resid 1274 through 1276' Processing helix chain 'I' and resid 1292 through 1317 removed outlier: 3.538A pdb=" N LEU I1296 " --> pdb=" O THR I1292 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR I1317 " --> pdb=" O GLU I1313 " (cutoff:3.500A) Processing helix chain 'I' and resid 1342 through 1359 removed outlier: 3.754A pdb=" N ALA I1346 " --> pdb=" O GLY I1342 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU I1359 " --> pdb=" O LYS I1355 " (cutoff:3.500A) Processing helix chain 'I' and resid 1369 through 1381 Processing helix chain 'I' and resid 1400 through 1427 removed outlier: 4.586A pdb=" N ARG I1410 " --> pdb=" O LYS I1406 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU I1411 " --> pdb=" O GLY I1407 " (cutoff:3.500A) Processing helix chain 'I' and resid 1448 through 1476 Processing helix chain 'I' and resid 1499 through 1530 removed outlier: 3.718A pdb=" N ARG I1503 " --> pdb=" O GLY I1499 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN I1517 " --> pdb=" O SER I1513 " (cutoff:3.500A) Processing helix chain 'I' and resid 1534 through 1543 Processing helix chain 'I' and resid 1559 through 1564 Processing helix chain 'I' and resid 1567 through 1571 removed outlier: 3.548A pdb=" N SER I1571 " --> pdb=" O GLY I1568 " (cutoff:3.500A) Processing helix chain 'I' and resid 1625 through 1630 Processing helix chain 'I' and resid 1635 through 1643 removed outlier: 3.586A pdb=" N ILE I1639 " --> pdb=" O GLU I1635 " (cutoff:3.500A) Processing helix chain 'I' and resid 1650 through 1674 Processing helix chain 'I' and resid 1679 through 1703 Processing helix chain 'I' and resid 1710 through 1725 Processing helix chain 'I' and resid 1730 through 1744 Processing helix chain 'I' and resid 1756 through 1776 removed outlier: 5.015A pdb=" N TRP I1761 " --> pdb=" O ARG I1757 " (cutoff:3.500A) Processing helix chain 'I' and resid 1793 through 1821 Processing helix chain 'I' and resid 1838 through 1850 Processing helix chain 'I' and resid 1851 through 1865 removed outlier: 3.561A pdb=" N GLU I1855 " --> pdb=" O PRO I1851 " (cutoff:3.500A) Processing helix chain 'I' and resid 1887 through 1896 removed outlier: 3.580A pdb=" N TYR I1891 " --> pdb=" O THR I1887 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS I1896 " --> pdb=" O LEU I1892 " (cutoff:3.500A) Processing helix chain 'I' and resid 1942 through 1948 removed outlier: 3.565A pdb=" N ASN I1948 " --> pdb=" O ASN I1944 " (cutoff:3.500A) Processing helix chain 'I' and resid 1951 through 1956 removed outlier: 3.725A pdb=" N ALA I1956 " --> pdb=" O LYS I1952 " (cutoff:3.500A) Processing helix chain 'I' and resid 1957 through 1983 Processing helix chain 'I' and resid 2025 through 2030 removed outlier: 3.871A pdb=" N ASP I2028 " --> pdb=" O ASN I2025 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG I2030 " --> pdb=" O MET I2027 " (cutoff:3.500A) Processing helix chain 'I' and resid 2042 through 2047 removed outlier: 4.107A pdb=" N ARG I2046 " --> pdb=" O PRO I2042 " (cutoff:3.500A) Processing helix chain 'I' and resid 2066 through 2077 removed outlier: 3.815A pdb=" N GLU I2077 " --> pdb=" O GLY I2073 " (cutoff:3.500A) Processing helix chain 'I' and resid 2083 through 2088 Processing helix chain 'I' and resid 2090 through 2110 removed outlier: 4.263A pdb=" N ALA I2094 " --> pdb=" O ASP I2090 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE I2108 " --> pdb=" O ASP I2104 " (cutoff:3.500A) Processing helix chain 'I' and resid 2121 through 2132 removed outlier: 4.251A pdb=" N ILE I2125 " --> pdb=" O LYS I2121 " (cutoff:3.500A) Processing helix chain 'I' and resid 2139 through 2161 removed outlier: 3.627A pdb=" N ASP I2143 " --> pdb=" O LYS I2139 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP I2144 " --> pdb=" O LYS I2140 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS I2149 " --> pdb=" O TRP I2145 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYS I2150 " --> pdb=" O LYS I2146 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE I2152 " --> pdb=" O ASN I2148 " (cutoff:3.500A) Processing helix chain 'I' and resid 2169 through 2174 Processing helix chain 'I' and resid 2182 through 2209 removed outlier: 3.672A pdb=" N GLN I2200 " --> pdb=" O CYS I2196 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU I2201 " --> pdb=" O ILE I2197 " (cutoff:3.500A) Processing helix chain 'I' and resid 2224 through 2244 removed outlier: 3.781A pdb=" N SER I2228 " --> pdb=" O ASN I2224 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP I2236 " --> pdb=" O LYS I2232 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP I2244 " --> pdb=" O ARG I2240 " (cutoff:3.500A) Processing helix chain 'I' and resid 2245 through 2249 Processing helix chain 'J' and resid 65 through 69 Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 420 Processing helix chain 'K' and resid 460 through 465 Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'K' and resid 553 through 557 removed outlier: 3.955A pdb=" N GLY K 557 " --> pdb=" O LYS K 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 Processing helix chain 'L' and resid 496 through 500 Processing helix chain 'M' and resid 971 through 977 removed outlier: 3.762A pdb=" N ASP M 977 " --> pdb=" O GLU M 973 " (cutoff:3.500A) Processing helix chain 'M' and resid 1027 through 1051 removed outlier: 3.685A pdb=" N GLU M1047 " --> pdb=" O GLN M1043 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN M1048 " --> pdb=" O TYR M1044 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR M1051 " --> pdb=" O GLU M1047 " (cutoff:3.500A) Processing helix chain 'M' and resid 1094 through 1125 Processing helix chain 'M' and resid 1142 through 1157 removed outlier: 4.150A pdb=" N TYR M1153 " --> pdb=" O CYS M1149 " (cutoff:3.500A) Processing helix chain 'M' and resid 1172 through 1180 Processing helix chain 'M' and resid 1189 through 1199 Processing helix chain 'M' and resid 1266 through 1271 removed outlier: 3.619A pdb=" N GLN M1270 " --> pdb=" O PRO M1266 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN M1271 " --> pdb=" O PRO M1267 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1266 through 1271' Processing helix chain 'M' and resid 1274 through 1278 removed outlier: 3.896A pdb=" N LEU M1277 " --> pdb=" O VAL M1274 " (cutoff:3.500A) Processing helix chain 'M' and resid 1292 through 1317 removed outlier: 3.642A pdb=" N THR M1317 " --> pdb=" O GLU M1313 " (cutoff:3.500A) Processing helix chain 'M' and resid 1343 through 1359 removed outlier: 4.074A pdb=" N LEU M1359 " --> pdb=" O LYS M1355 " (cutoff:3.500A) Processing helix chain 'M' and resid 1368 through 1381 removed outlier: 3.615A pdb=" N LEU M1372 " --> pdb=" O HIS M1368 " (cutoff:3.500A) Processing helix chain 'M' and resid 1400 through 1427 removed outlier: 4.675A pdb=" N ARG M1410 " --> pdb=" O LYS M1406 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU M1411 " --> pdb=" O GLY M1407 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN M1427 " --> pdb=" O ILE M1423 " (cutoff:3.500A) Processing helix chain 'M' and resid 1448 through 1476 removed outlier: 3.507A pdb=" N SER M1452 " --> pdb=" O ASP M1448 " (cutoff:3.500A) Processing helix chain 'M' and resid 1499 through 1530 removed outlier: 3.955A pdb=" N GLN M1517 " --> pdb=" O SER M1513 " (cutoff:3.500A) Processing helix chain 'M' and resid 1534 through 1543 Processing helix chain 'M' and resid 1559 through 1564 Processing helix chain 'M' and resid 1567 through 1571 removed outlier: 3.569A pdb=" N SER M1571 " --> pdb=" O GLY M1568 " (cutoff:3.500A) Processing helix chain 'M' and resid 1589 through 1593 removed outlier: 4.346A pdb=" N ASN M1592 " --> pdb=" O LYS M1589 " (cutoff:3.500A) Processing helix chain 'M' and resid 1625 through 1630 Processing helix chain 'M' and resid 1633 through 1636 Processing helix chain 'M' and resid 1637 through 1643 removed outlier: 4.021A pdb=" N ILE M1641 " --> pdb=" O PHE M1637 " (cutoff:3.500A) Processing helix chain 'M' and resid 1649 through 1674 removed outlier: 4.315A pdb=" N GLU M1653 " --> pdb=" O LYS M1649 " (cutoff:3.500A) Processing helix chain 'M' and resid 1679 through 1703 Processing helix chain 'M' and resid 1710 through 1725 Processing helix chain 'M' and resid 1730 through 1744 removed outlier: 3.839A pdb=" N TRP M1741 " --> pdb=" O ALA M1737 " (cutoff:3.500A) Processing helix chain 'M' and resid 1756 through 1776 removed outlier: 5.135A pdb=" N TRP M1761 " --> pdb=" O ARG M1757 " (cutoff:3.500A) Processing helix chain 'M' and resid 1793 through 1821 Processing helix chain 'M' and resid 1838 through 1865 Proline residue: M1851 - end of helix removed outlier: 4.378A pdb=" N ILE M1854 " --> pdb=" O ASN M1850 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS M1865 " --> pdb=" O ASN M1861 " (cutoff:3.500A) Processing helix chain 'M' and resid 1887 through 1896 removed outlier: 3.758A pdb=" N CYS M1896 " --> pdb=" O LEU M1892 " (cutoff:3.500A) Processing helix chain 'M' and resid 1942 through 1948 removed outlier: 3.616A pdb=" N ASN M1948 " --> pdb=" O ASN M1944 " (cutoff:3.500A) Processing helix chain 'M' and resid 1952 through 1956 removed outlier: 3.517A pdb=" N ALA M1956 " --> pdb=" O LYS M1953 " (cutoff:3.500A) Processing helix chain 'M' and resid 1957 through 1984 removed outlier: 3.795A pdb=" N CYS M1961 " --> pdb=" O HIS M1957 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS M1984 " --> pdb=" O ILE M1980 " (cutoff:3.500A) Processing helix chain 'M' and resid 2026 through 2030 removed outlier: 3.649A pdb=" N ARG M2030 " --> pdb=" O MET M2027 " (cutoff:3.500A) Processing helix chain 'M' and resid 2042 through 2047 Processing helix chain 'M' and resid 2066 through 2076 removed outlier: 3.756A pdb=" N GLY M2073 " --> pdb=" O GLU M2069 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN M2075 " --> pdb=" O LEU M2071 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER M2076 " --> pdb=" O LYS M2072 " (cutoff:3.500A) Processing helix chain 'M' and resid 2083 through 2088 Processing helix chain 'M' and resid 2090 through 2110 Processing helix chain 'M' and resid 2121 through 2132 removed outlier: 4.418A pdb=" N ILE M2125 " --> pdb=" O LYS M2121 " (cutoff:3.500A) Processing helix chain 'M' and resid 2139 through 2162 removed outlier: 3.586A pdb=" N TRP M2144 " --> pdb=" O LYS M2140 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS M2149 " --> pdb=" O TRP M2145 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS M2150 " --> pdb=" O LYS M2146 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU M2157 " --> pdb=" O TRP M2153 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS M2158 " --> pdb=" O ASN M2154 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY M2159 " --> pdb=" O ALA M2155 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS M2161 " --> pdb=" O LEU M2157 " (cutoff:3.500A) Processing helix chain 'M' and resid 2169 through 2174 Processing helix chain 'M' and resid 2182 through 2209 removed outlier: 3.734A pdb=" N ILE M2188 " --> pdb=" O PHE M2184 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE M2197 " --> pdb=" O THR M2193 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN M2198 " --> pdb=" O ASN M2194 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU M2201 " --> pdb=" O ILE M2197 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL M2206 " --> pdb=" O HIS M2202 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS M2207 " --> pdb=" O LYS M2203 " (cutoff:3.500A) Processing helix chain 'M' and resid 2223 through 2242 removed outlier: 4.131A pdb=" N THR M2227 " --> pdb=" O SER M2223 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER M2228 " --> pdb=" O ASN M2224 " (cutoff:3.500A) Processing helix chain 'M' and resid 2243 through 2249 removed outlier: 3.938A pdb=" N THR M2246 " --> pdb=" O GLN M2243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.809A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.809A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.686A pdb=" N GLN A 487 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 562 removed outlier: 3.639A pdb=" N TYR A 562 " --> pdb=" O LEU B 561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.525A pdb=" N VAL A 567 " --> pdb=" O TYR J 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.582A pdb=" N LEU B 365 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B 369 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 407 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 378 through 383 Processing sheet with id=AA8, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.729A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.729A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB2, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.754A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP C 371 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE C 405 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR C 404 " --> pdb=" O HIS C 400 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 379 through 384 Processing sheet with id=AB4, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.563A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.563A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 516 " --> pdb=" O MET C 506 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET C 506 " --> pdb=" O PHE C 516 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.653A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 379 through 383 Processing sheet with id=AB9, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.612A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC2, first strand: chain 'D' and resid 565 through 567 Processing sheet with id=AC3, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.755A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR E 363 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 413 " --> pdb=" O THR E 363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 379 through 383 Processing sheet with id=AC5, first strand: chain 'E' and resid 453 through 457 Processing sheet with id=AC6, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.556A pdb=" N PHE E 516 " --> pdb=" O MET E 506 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET E 506 " --> pdb=" O PHE E 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AC8, first strand: chain 'F' and resid 347 through 350 removed outlier: 4.093A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 379 through 383 removed outlier: 3.604A pdb=" N CYS F 426 " --> pdb=" O GLN F 439 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN F 439 " --> pdb=" O CYS F 426 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.848A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.848A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD4, first strand: chain 'F' and resid 565 through 567 removed outlier: 6.463A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN H 563 " --> pdb=" O VAL K 564 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LEU K 566 " --> pdb=" O ASN H 563 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER H 565 " --> pdb=" O LEU K 566 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU L 566 " --> pdb=" O ASN K 563 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER K 565 " --> pdb=" O LEU L 566 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 346 through 350 removed outlier: 3.749A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N THR G 366 " --> pdb=" O ALA G 411 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ALA G 411 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU G 368 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY G 409 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N THR G 370 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA G 407 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU G 372 " --> pdb=" O PHE G 405 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 379 through 383 Processing sheet with id=AD7, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.611A pdb=" N THR G 473 " --> pdb=" O LEU G 457 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.611A pdb=" N THR G 473 " --> pdb=" O LEU G 457 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE G 516 " --> pdb=" O MET G 506 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET G 506 " --> pdb=" O PHE G 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AE1, first strand: chain 'H' and resid 346 through 350 removed outlier: 3.864A pdb=" N THR H 366 " --> pdb=" O ILE H 350 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP H 371 " --> pdb=" O PHE H 405 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE H 405 " --> pdb=" O ASP H 371 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 424 through 425 Processing sheet with id=AE3, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.600A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.600A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.706A pdb=" N CYS H 536 " --> pdb=" O ARG H 550 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG H 550 " --> pdb=" O CYS H 536 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 1278 through 1279 Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.946A pdb=" N THR J 18 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN J 36 " --> pdb=" O THR J 18 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE J 22 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 347 through 350 removed outlier: 4.090A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP K 371 " --> pdb=" O PHE K 405 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE K 405 " --> pdb=" O ASP K 371 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 391 through 392 removed outlier: 3.961A pdb=" N LYS K 391 " --> pdb=" O TRP K 382 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP K 382 " --> pdb=" O LYS K 391 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.641A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.641A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AF4, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.675A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR L 477 " --> pdb=" O ALA L 517 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA L 517 " --> pdb=" O THR L 477 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 469 through 470 Processing sheet with id=AF6, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AF7, first strand: chain 'L' and resid 501 through 502 1511 hydrogen bonds defined for protein. 4146 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: 8.23 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.55: 35818 1.55 - 1.88: 297 1.88 - 2.20: 0 2.20 - 2.53: 0 2.53 - 2.86: 2 Bond restraints: 36117 Sorted by residual: bond pdb=" C PHE M1551 " pdb=" N PHE M1553 " ideal model delta sigma weight residual 1.332 2.856 -1.524 1.40e-02 5.10e+03 1.18e+04 bond pdb=" C PHE I1551 " pdb=" N PHE I1553 " ideal model delta sigma weight residual 1.332 2.842 -1.509 1.40e-02 5.10e+03 1.16e+04 bond pdb=" N ARG B 491 " pdb=" CA ARG B 491 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.73e+00 bond pdb=" C GLU M1514 " pdb=" O GLU M1514 " ideal model delta sigma weight residual 1.237 1.252 -0.015 1.19e-02 7.06e+03 1.59e+00 bond pdb=" CB MET M 982 " pdb=" CG MET M 982 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.56e+00 ... (remaining 36112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.47: 48910 11.47 - 22.93: 3 22.93 - 34.40: 2 34.40 - 45.86: 0 45.86 - 57.33: 2 Bond angle restraints: 48917 Sorted by residual: angle pdb=" O PHE I1551 " pdb=" C PHE I1551 " pdb=" N PHE I1553 " ideal model delta sigma weight residual 122.59 65.26 57.33 1.33e+00 5.65e-01 1.86e+03 angle pdb=" O PHE M1551 " pdb=" C PHE M1551 " pdb=" N PHE M1553 " ideal model delta sigma weight residual 122.29 66.87 55.42 1.40e+00 5.10e-01 1.57e+03 angle pdb=" CA PHE M1551 " pdb=" C PHE M1551 " pdb=" N PHE M1553 " ideal model delta sigma weight residual 115.29 134.72 -19.43 1.18e+00 7.18e-01 2.71e+02 angle pdb=" C PHE M1551 " pdb=" N PHE M1553 " pdb=" CA PHE M1553 " ideal model delta sigma weight residual 121.54 147.30 -25.76 1.91e+00 2.74e-01 1.82e+02 angle pdb=" C PHE I1551 " pdb=" N PHE I1553 " pdb=" CA PHE I1553 " ideal model delta sigma weight residual 121.54 145.35 -23.81 1.91e+00 2.74e-01 1.55e+02 ... (remaining 48912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.10: 20817 25.10 - 50.21: 1181 50.21 - 75.31: 79 75.31 - 100.42: 10 100.42 - 125.52: 2 Dihedral angle restraints: 22089 sinusoidal: 9159 harmonic: 12930 Sorted by residual: dihedral pdb=" CA PHE M1551 " pdb=" C PHE M1551 " pdb=" N PHE M1553 " pdb=" CA PHE M1553 " ideal model delta harmonic sigma weight residual -180.00 -54.48 -125.52 0 5.00e+00 4.00e-02 6.30e+02 dihedral pdb=" CA PHE I1551 " pdb=" C PHE I1551 " pdb=" N PHE I1553 " pdb=" CA PHE I1553 " ideal model delta harmonic sigma weight residual -180.00 -57.43 -122.57 0 5.00e+00 4.00e-02 6.01e+02 dihedral pdb=" CB CYS M2210 " pdb=" SG CYS M2210 " pdb=" SG CYS M2226 " pdb=" CB CYS M2226 " ideal model delta sinusoidal sigma weight residual -86.00 -18.74 -67.26 1 1.00e+01 1.00e-02 5.89e+01 ... (remaining 22086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4197 0.048 - 0.096: 912 0.096 - 0.144: 239 0.144 - 0.192: 3 0.192 - 0.239: 1 Chirality restraints: 5352 Sorted by residual: chirality pdb=" CB ILE I1288 " pdb=" CA ILE I1288 " pdb=" CG1 ILE I1288 " pdb=" CG2 ILE I1288 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA GLU M1367 " pdb=" N GLU M1367 " pdb=" C GLU M1367 " pdb=" CB GLU M1367 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE F 380 " pdb=" N ILE F 380 " pdb=" C ILE F 380 " pdb=" CB ILE F 380 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 5349 not shown) Planarity restraints: 6261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE M1551 " 0.187 2.00e-02 2.50e+03 2.28e-01 5.19e+02 pdb=" C PHE M1551 " -0.386 2.00e-02 2.50e+03 pdb=" O PHE M1551 " 0.141 2.00e-02 2.50e+03 pdb=" N PHE M1553 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I1551 " -0.188 2.00e-02 2.50e+03 2.24e-01 5.03e+02 pdb=" C PHE I1551 " 0.381 2.00e-02 2.50e+03 pdb=" O PHE I1551 " -0.131 2.00e-02 2.50e+03 pdb=" N PHE I1553 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I2244 " 0.022 2.00e-02 2.50e+03 1.83e-02 8.36e+00 pdb=" CG TRP I2244 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP I2244 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP I2244 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I2244 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I2244 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I2244 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP I2244 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I2244 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I2244 " 0.005 2.00e-02 2.50e+03 ... (remaining 6258 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 514 2.59 - 3.17: 32221 3.17 - 3.75: 57813 3.75 - 4.32: 73502 4.32 - 4.90: 117247 Nonbonded interactions: 281297 Sorted by model distance: nonbonded pdb=" OE1 GLU D 527 " pdb=" OH TYR D 534 " model vdw 2.017 3.040 nonbonded pdb=" O MET B 489 " pdb=" OG1 THR B 535 " model vdw 2.084 3.040 nonbonded pdb=" O LEU I2029 " pdb=" OG1 THR I2032 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR C 533 " pdb=" OG1 THR C 551 " model vdw 2.143 3.040 nonbonded pdb=" NE2 GLN M2075 " pdb=" O ALA M2155 " model vdw 2.159 3.120 ... (remaining 281292 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 449 through 520 or resid 522 through 576)) selection = chain 'L' } ncs_group { reference = (chain 'B' and (resid 345 through 444 or resid 449 through 568)) selection = (chain 'C' and (resid 345 through 444 or resid 449 through 568)) selection = (chain 'D' and (resid 345 through 444 or resid 449 through 568)) selection = (chain 'E' and (resid 345 through 444 or resid 449 through 568)) selection = (chain 'F' and (resid 345 through 444 or resid 449 through 568)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 568)) selection = (chain 'H' and (resid 345 through 444 or resid 449 through 568)) selection = (chain 'K' and (resid 345 through 444 or resid 449 through 568)) } ncs_group { reference = chain 'I' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.950 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.012 1.524 36180 Z= 0.814 Angle : 0.741 57.331 49043 Z= 0.438 Chirality : 0.042 0.239 5352 Planarity : 0.006 0.228 6261 Dihedral : 14.009 125.521 13522 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.10 % Favored : 90.88 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -0.64 (0.13), residues: 4308 helix: 0.88 (0.14), residues: 1335 sheet: 0.35 (0.19), residues: 736 loop : -1.57 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 461 TYR 0.027 0.001 TYR F 534 PHE 0.020 0.001 PHE G 358 TRP 0.049 0.001 TRP I2244 HIS 0.005 0.001 HIS I1368 Details of bonding type rmsd covalent geometry : bond 0.01152 (36117) covalent geometry : angle 0.73957 (48917) SS BOND : bond 0.00306 ( 63) SS BOND : angle 1.06140 ( 126) hydrogen bonds : bond 0.16461 ( 1406) hydrogen bonds : angle 6.41930 ( 4146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8616 Ramachandran restraints generated. 4308 Oldfield, 0 Emsley, 4308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8616 Ramachandran restraints generated. 4308 Oldfield, 0 Emsley, 4308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 TYR cc_start: 0.9466 (t80) cc_final: 0.9261 (t80) REVERT: B 493 GLN cc_start: 0.8596 (mp10) cc_final: 0.8329 (mp10) REVERT: B 553 ASP cc_start: 0.7997 (t70) cc_final: 0.7740 (t0) REVERT: C 453 ASP cc_start: 0.8486 (m-30) cc_final: 0.8262 (m-30) REVERT: D 465 ASN cc_start: 0.8807 (m110) cc_final: 0.8357 (m110) REVERT: D 549 GLU cc_start: 0.8221 (pm20) cc_final: 0.8014 (pm20) REVERT: I 1357 MET cc_start: 0.9552 (tmm) cc_final: 0.9192 (tmm) REVERT: I 1859 MET cc_start: 0.8639 (pmm) cc_final: 0.8392 (pmm) REVERT: I 1959 MET cc_start: 0.5331 (mmp) cc_final: 0.4949 (tpp) REVERT: K 465 ASN cc_start: 0.9363 (p0) cc_final: 0.9117 (p0) REVERT: L 506 MET cc_start: 0.8925 (mpp) cc_final: 0.8705 (mpp) REVERT: M 1357 MET cc_start: 0.9203 (tmm) cc_final: 0.8993 (tmm) REVERT: M 1412 MET cc_start: 0.9029 (mmp) cc_final: 0.8759 (mmm) REVERT: M 1859 MET cc_start: 0.9315 (mtm) cc_final: 0.8991 (mtm) REVERT: M 1862 TYR cc_start: 0.8849 (t80) cc_final: 0.8323 (t80) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2392 time to fit residues: 97.4886 Evaluate side-chains 187 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 ASN ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 971 ASN ** I1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1629 GLN I1709 HIS I1957 HIS ** I2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN L 518 HIS L 563 ASN ** M1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1225 ASN M1522 GLN ** M1850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M2212 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.058252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.042115 restraints weight = 296301.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.043370 restraints weight = 165335.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.044161 restraints weight = 115903.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.044644 restraints weight = 92630.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.044929 restraints weight = 80790.485| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36180 Z= 0.130 Angle : 0.620 8.498 49043 Z= 0.321 Chirality : 0.043 0.209 5352 Planarity : 0.004 0.063 6261 Dihedral : 4.383 31.148 4742 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.81 % Favored : 91.12 % Rotamer: Outliers : 0.38 % Allowed : 7.77 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.70 (0.13), residues: 4312 helix: 0.77 (0.14), residues: 1402 sheet: 0.51 (0.19), residues: 727 loop : -1.71 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 346 TYR 0.019 0.001 TYR F 534 PHE 0.020 0.001 PHE B 358 TRP 0.035 0.001 TRP I2244 HIS 0.005 0.001 HIS K 518 Details of bonding type rmsd covalent geometry : bond 0.00271 (36117) covalent geometry : angle 0.61861 (48917) SS BOND : bond 0.00409 ( 63) SS BOND : angle 1.07508 ( 126) hydrogen bonds : bond 0.04949 ( 1406) hydrogen bonds : angle 5.09079 ( 4146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 PHE cc_start: 0.9108 (p90) cc_final: 0.8725 (p90) REVERT: B 375 TYR cc_start: 0.9450 (t80) cc_final: 0.9225 (t80) REVERT: B 493 GLN cc_start: 0.8899 (mp10) cc_final: 0.8556 (mp10) REVERT: B 553 ASP cc_start: 0.8339 (t70) cc_final: 0.8027 (t0) REVERT: C 453 ASP cc_start: 0.8770 (m-30) cc_final: 0.8480 (m-30) REVERT: D 465 ASN cc_start: 0.8876 (m110) cc_final: 0.8476 (m110) REVERT: G 453 ASP cc_start: 0.8985 (t0) cc_final: 0.8675 (t0) REVERT: H 534 TYR cc_start: 0.8795 (m-10) cc_final: 0.8524 (m-10) REVERT: I 1313 GLU cc_start: 0.8800 (pp20) cc_final: 0.8498 (pp20) REVERT: I 1357 MET cc_start: 0.9656 (tmm) cc_final: 0.9296 (tmm) REVERT: I 1959 MET cc_start: 0.5213 (mmp) cc_final: 0.4890 (tpp) REVERT: I 2013 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8394 (pttt) REVERT: K 506 MET cc_start: 0.8707 (tpp) cc_final: 0.8410 (tpp) REVERT: L 568 MET cc_start: 0.8020 (ppp) cc_final: 0.7803 (ppp) REVERT: M 1357 MET cc_start: 0.9355 (tmm) cc_final: 0.9068 (tmm) REVERT: M 1412 MET cc_start: 0.9140 (mmp) cc_final: 0.8871 (mmm) REVERT: M 1783 MET cc_start: 0.5913 (ttt) cc_final: 0.5078 (tpt) REVERT: M 1859 MET cc_start: 0.9342 (mtm) cc_final: 0.9096 (mtm) REVERT: M 1862 TYR cc_start: 0.8908 (t80) cc_final: 0.8282 (t80) REVERT: M 1884 MET cc_start: 0.8593 (tmm) cc_final: 0.8356 (tmm) REVERT: M 2126 LYS cc_start: 0.9570 (tptp) cc_final: 0.9332 (tppt) outliers start: 15 outliers final: 9 residues processed: 227 average time/residue: 0.2216 time to fit residues: 81.5825 Evaluate side-chains 208 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain I residue 2154 ASN Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain M residue 1036 GLU Chi-restraints excluded: chain M residue 1537 ASP Chi-restraints excluded: chain M residue 2153 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 72 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 59 optimal weight: 30.0000 chunk 92 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 432 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 362 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN G 463 GLN G 529 ASN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 971 ASN ** I1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1857 ASN I1901 ASN I2194 ASN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1125 GLN ** M1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1305 HIS ** M1850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1864 ASN ** M1978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M2219 GLN ** M2243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.055596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.039644 restraints weight = 312750.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.041046 restraints weight = 179137.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.041261 restraints weight = 108587.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.041333 restraints weight = 115370.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.041371 restraints weight = 98930.858| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 36180 Z= 0.295 Angle : 0.707 10.082 49043 Z= 0.373 Chirality : 0.045 0.291 5352 Planarity : 0.005 0.102 6261 Dihedral : 4.804 25.892 4742 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.34 % Favored : 89.56 % Rotamer: Outliers : 1.08 % Allowed : 11.70 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -1.00 (0.13), residues: 4312 helix: 0.52 (0.13), residues: 1436 sheet: -0.04 (0.19), residues: 756 loop : -1.78 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 461 TYR 0.036 0.002 TYR B 534 PHE 0.025 0.002 PHE M1551 TRP 0.032 0.002 TRP I2244 HIS 0.007 0.001 HIS G 540 Details of bonding type rmsd covalent geometry : bond 0.00627 (36117) covalent geometry : angle 0.70443 (48917) SS BOND : bond 0.00556 ( 63) SS BOND : angle 1.34632 ( 126) hydrogen bonds : bond 0.05210 ( 1406) hydrogen bonds : angle 5.22267 ( 4146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LYS cc_start: 0.8637 (tmtt) cc_final: 0.8417 (tptp) REVERT: B 375 TYR cc_start: 0.9434 (t80) cc_final: 0.9193 (t80) REVERT: B 493 GLN cc_start: 0.9066 (mp10) cc_final: 0.8764 (mp10) REVERT: B 553 ASP cc_start: 0.8641 (t70) cc_final: 0.8421 (t0) REVERT: C 453 ASP cc_start: 0.8946 (m-30) cc_final: 0.8726 (m-30) REVERT: C 530 THR cc_start: 0.9586 (OUTLIER) cc_final: 0.9347 (p) REVERT: D 465 ASN cc_start: 0.8933 (m110) cc_final: 0.8494 (m110) REVERT: D 549 GLU cc_start: 0.8444 (pm20) cc_final: 0.8146 (pm20) REVERT: E 499 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8947 (mmmt) REVERT: G 453 ASP cc_start: 0.8974 (t0) cc_final: 0.8656 (t0) REVERT: H 465 ASN cc_start: 0.9244 (m110) cc_final: 0.8440 (m-40) REVERT: I 1357 MET cc_start: 0.9618 (tmm) cc_final: 0.9251 (tmm) REVERT: I 1764 MET cc_start: 0.9199 (mtt) cc_final: 0.8547 (ppp) REVERT: I 1859 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7986 (pmm) REVERT: I 1959 MET cc_start: 0.4669 (mmp) cc_final: 0.4369 (tpp) REVERT: I 2013 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8356 (pttt) REVERT: K 506 MET cc_start: 0.8997 (tpp) cc_final: 0.8702 (tpp) REVERT: L 568 MET cc_start: 0.8293 (ppp) cc_final: 0.7929 (ppp) REVERT: M 1272 LEU cc_start: 0.9420 (tp) cc_final: 0.9216 (tp) REVERT: M 1357 MET cc_start: 0.9396 (tmm) cc_final: 0.9077 (tmm) REVERT: M 1412 MET cc_start: 0.9201 (mmp) cc_final: 0.8919 (mmm) REVERT: M 1862 TYR cc_start: 0.9030 (t80) cc_final: 0.8421 (t80) REVERT: M 2126 LYS cc_start: 0.9562 (tptp) cc_final: 0.9350 (tppt) REVERT: M 2156 MET cc_start: 0.9078 (mpp) cc_final: 0.8733 (mpp) outliers start: 43 outliers final: 24 residues processed: 223 average time/residue: 0.2060 time to fit residues: 75.6281 Evaluate side-chains 207 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain I residue 1859 MET Chi-restraints excluded: chain I residue 1888 VAL Chi-restraints excluded: chain I residue 2071 LEU Chi-restraints excluded: chain I residue 2154 ASN Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain L residue 464 LEU Chi-restraints excluded: chain L residue 474 CYS Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain M residue 1036 GLU Chi-restraints excluded: chain M residue 1537 ASP Chi-restraints excluded: chain M residue 1553 PHE Chi-restraints excluded: chain M residue 1554 ILE Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 2066 PHE Chi-restraints excluded: chain M residue 2153 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 12 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 425 optimal weight: 8.9990 chunk 97 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 971 ASN ** I1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2212 ASN I2219 GLN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS ** M1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.057447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.041154 restraints weight = 294984.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.042401 restraints weight = 165656.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.043181 restraints weight = 115837.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.043661 restraints weight = 92932.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.043910 restraints weight = 81292.722| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36180 Z= 0.115 Angle : 0.606 11.311 49043 Z= 0.310 Chirality : 0.043 0.168 5352 Planarity : 0.004 0.085 6261 Dihedral : 4.505 25.970 4742 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.67 % Favored : 91.23 % Rotamer: Outliers : 1.06 % Allowed : 13.85 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -0.77 (0.13), residues: 4312 helix: 0.75 (0.14), residues: 1410 sheet: 0.39 (0.20), residues: 712 loop : -1.73 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 461 TYR 0.026 0.001 TYR B 534 PHE 0.022 0.001 PHE B 358 TRP 0.023 0.001 TRP I2244 HIS 0.005 0.001 HIS I1368 Details of bonding type rmsd covalent geometry : bond 0.00240 (36117) covalent geometry : angle 0.60521 (48917) SS BOND : bond 0.00385 ( 63) SS BOND : angle 0.94458 ( 126) hydrogen bonds : bond 0.04224 ( 1406) hydrogen bonds : angle 4.74880 ( 4146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 PHE cc_start: 0.9249 (p90) cc_final: 0.8887 (p90) REVERT: B 375 TYR cc_start: 0.9469 (t80) cc_final: 0.9233 (t80) REVERT: B 493 GLN cc_start: 0.8886 (mp10) cc_final: 0.8560 (mp10) REVERT: B 553 ASP cc_start: 0.8383 (t70) cc_final: 0.8153 (t0) REVERT: C 453 ASP cc_start: 0.8827 (m-30) cc_final: 0.8606 (m-30) REVERT: D 465 ASN cc_start: 0.8945 (m110) cc_final: 0.8532 (m110) REVERT: G 453 ASP cc_start: 0.8958 (t0) cc_final: 0.8618 (t0) REVERT: I 1313 GLU cc_start: 0.8950 (pp20) cc_final: 0.8624 (pp20) REVERT: I 1357 MET cc_start: 0.9614 (tmm) cc_final: 0.9221 (tmm) REVERT: I 1764 MET cc_start: 0.9084 (mtt) cc_final: 0.8459 (ppp) REVERT: I 1859 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7980 (pmm) REVERT: I 1959 MET cc_start: 0.4809 (mmp) cc_final: 0.4444 (tpp) REVERT: I 2013 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8289 (pttt) REVERT: I 2132 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8897 (tm-30) REVERT: K 506 MET cc_start: 0.8927 (tpp) cc_final: 0.8633 (tpp) REVERT: L 568 MET cc_start: 0.8198 (ppp) cc_final: 0.7762 (ppp) REVERT: M 1357 MET cc_start: 0.9400 (tmm) cc_final: 0.9100 (tmm) REVERT: M 1412 MET cc_start: 0.9153 (mmp) cc_final: 0.8888 (mmm) REVERT: M 1783 MET cc_start: 0.5800 (ttt) cc_final: 0.4307 (tpt) REVERT: M 1800 GLU cc_start: 0.9534 (OUTLIER) cc_final: 0.9306 (mm-30) REVERT: M 1859 MET cc_start: 0.9432 (mtm) cc_final: 0.9074 (mtm) REVERT: M 1862 TYR cc_start: 0.8959 (t80) cc_final: 0.8288 (t80) REVERT: M 1884 MET cc_start: 0.8603 (tmm) cc_final: 0.8325 (tmm) REVERT: M 2126 LYS cc_start: 0.9544 (tptp) cc_final: 0.9314 (tppt) outliers start: 42 outliers final: 18 residues processed: 242 average time/residue: 0.2026 time to fit residues: 79.9698 Evaluate side-chains 212 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain I residue 1859 MET Chi-restraints excluded: chain I residue 2071 LEU Chi-restraints excluded: chain I residue 2132 GLU Chi-restraints excluded: chain I residue 2154 ASN Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain L residue 464 LEU Chi-restraints excluded: chain L residue 474 CYS Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain M residue 1537 ASP Chi-restraints excluded: chain M residue 1553 PHE Chi-restraints excluded: chain M residue 1800 GLU Chi-restraints excluded: chain M residue 1887 THR Chi-restraints excluded: chain M residue 2153 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 85 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 403 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 422 optimal weight: 0.6980 chunk 355 optimal weight: 0.8980 chunk 306 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1744 ASN ** M1850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1978 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 = 0.3695 r_free = 0.3695 target = 0.056143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.040444 restraints weight = 299914.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.041421 restraints weight = 169937.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.041294 restraints weight = 111955.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.041559 restraints weight = 125198.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.041748 restraints weight = 105095.457| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36180 Z= 0.203 Angle : 0.640 10.905 49043 Z= 0.332 Chirality : 0.043 0.273 5352 Planarity : 0.004 0.066 6261 Dihedral : 4.571 25.010 4742 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.81 % Favored : 90.10 % Rotamer: Outliers : 1.36 % Allowed : 15.64 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -0.82 (0.13), residues: 4312 helix: 0.77 (0.14), residues: 1410 sheet: 0.12 (0.19), residues: 725 loop : -1.73 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 461 TYR 0.017 0.001 TYR B 455 PHE 0.020 0.001 PHE M1551 TRP 0.020 0.001 TRP I2244 HIS 0.006 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00436 (36117) covalent geometry : angle 0.63808 (48917) SS BOND : bond 0.00433 ( 63) SS BOND : angle 1.18385 ( 126) hydrogen bonds : bond 0.04432 ( 1406) hydrogen bonds : angle 4.87871 ( 4146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 PHE cc_start: 0.9257 (p90) cc_final: 0.8916 (p90) REVERT: B 375 TYR cc_start: 0.9432 (t80) cc_final: 0.9183 (t80) REVERT: B 493 GLN cc_start: 0.9006 (mp10) cc_final: 0.8798 (mp10) REVERT: C 453 ASP cc_start: 0.8933 (m-30) cc_final: 0.8720 (m-30) REVERT: C 530 THR cc_start: 0.9611 (OUTLIER) cc_final: 0.9394 (p) REVERT: C 561 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9215 (mm) REVERT: D 465 ASN cc_start: 0.8963 (m110) cc_final: 0.8514 (m110) REVERT: G 453 ASP cc_start: 0.8990 (t0) cc_final: 0.8647 (t0) REVERT: H 518 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7099 (m170) REVERT: I 1313 GLU cc_start: 0.8955 (pp20) cc_final: 0.8611 (pp20) REVERT: I 1357 MET cc_start: 0.9629 (tmm) cc_final: 0.9237 (tmm) REVERT: I 1359 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8762 (pp) REVERT: I 1764 MET cc_start: 0.9200 (mtt) cc_final: 0.8514 (ppp) REVERT: I 1859 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7995 (pmm) REVERT: I 1959 MET cc_start: 0.4435 (mmp) cc_final: 0.4103 (tpp) REVERT: I 2132 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.8833 (tp30) REVERT: K 506 MET cc_start: 0.9070 (tpp) cc_final: 0.8733 (tpp) REVERT: L 568 MET cc_start: 0.8294 (ppp) cc_final: 0.7827 (ppp) REVERT: M 1357 MET cc_start: 0.9461 (tmm) cc_final: 0.9129 (tmm) REVERT: M 1412 MET cc_start: 0.9176 (mmp) cc_final: 0.8899 (mmm) REVERT: M 1783 MET cc_start: 0.6060 (ttt) cc_final: 0.5380 (tpt) REVERT: M 1800 GLU cc_start: 0.9526 (OUTLIER) cc_final: 0.9321 (mm-30) REVERT: M 1859 MET cc_start: 0.9456 (mtm) cc_final: 0.9197 (mtm) REVERT: M 1862 TYR cc_start: 0.9007 (t80) cc_final: 0.8364 (t80) REVERT: M 1943 MET cc_start: 0.9181 (ppp) cc_final: 0.8947 (ppp) REVERT: M 2126 LYS cc_start: 0.9591 (tptp) cc_final: 0.9362 (tppt) outliers start: 54 outliers final: 33 residues processed: 238 average time/residue: 0.2142 time to fit residues: 82.8901 Evaluate side-chains 226 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain I residue 1349 ARG Chi-restraints excluded: chain I residue 1359 LEU Chi-restraints excluded: chain I residue 1859 MET Chi-restraints excluded: chain I residue 2071 LEU Chi-restraints excluded: chain I residue 2132 GLU Chi-restraints excluded: chain I residue 2154 ASN Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain L residue 464 LEU Chi-restraints excluded: chain L residue 474 CYS Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 1305 HIS Chi-restraints excluded: chain M residue 1367 GLU Chi-restraints excluded: chain M residue 1537 ASP Chi-restraints excluded: chain M residue 1553 PHE Chi-restraints excluded: chain M residue 1554 ILE Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1800 GLU Chi-restraints excluded: chain M residue 1887 THR Chi-restraints excluded: chain M residue 2153 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 294 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 289 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 201 optimal weight: 0.0470 chunk 213 optimal weight: 5.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1911 ASN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS ** M1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.056412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.040173 restraints weight = 307276.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.041402 restraints weight = 169956.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.042159 restraints weight = 118438.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.042614 restraints weight = 95224.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.042898 restraints weight = 83578.642| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36180 Z= 0.167 Angle : 0.632 12.043 49043 Z= 0.324 Chirality : 0.043 0.213 5352 Planarity : 0.004 0.057 6261 Dihedral : 4.582 25.265 4742 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.72 % Favored : 90.19 % Rotamer: Outliers : 1.64 % Allowed : 16.47 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -0.84 (0.13), residues: 4312 helix: 0.72 (0.14), residues: 1430 sheet: 0.13 (0.19), residues: 722 loop : -1.74 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 461 TYR 0.033 0.001 TYR B 534 PHE 0.026 0.001 PHE I2066 TRP 0.020 0.001 TRP I2244 HIS 0.005 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00360 (36117) covalent geometry : angle 0.63075 (48917) SS BOND : bond 0.00416 ( 63) SS BOND : angle 1.09761 ( 126) hydrogen bonds : bond 0.04284 ( 1406) hydrogen bonds : angle 4.80779 ( 4146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 PHE cc_start: 0.9273 (p90) cc_final: 0.8982 (p90) REVERT: B 375 TYR cc_start: 0.9462 (t80) cc_final: 0.9222 (t80) REVERT: B 493 GLN cc_start: 0.8936 (mp10) cc_final: 0.8720 (mp10) REVERT: C 453 ASP cc_start: 0.8959 (m-30) cc_final: 0.8734 (m-30) REVERT: C 530 THR cc_start: 0.9611 (OUTLIER) cc_final: 0.9391 (p) REVERT: C 561 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9210 (mm) REVERT: D 465 ASN cc_start: 0.8954 (m110) cc_final: 0.8497 (m110) REVERT: F 453 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8241 (t0) REVERT: G 453 ASP cc_start: 0.8991 (t0) cc_final: 0.8622 (t0) REVERT: H 489 MET cc_start: 0.7938 (tpp) cc_final: 0.7649 (tpp) REVERT: H 518 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7102 (m170) REVERT: I 1045 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8332 (mm-40) REVERT: I 1313 GLU cc_start: 0.8962 (pp20) cc_final: 0.8622 (pp20) REVERT: I 1349 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8516 (mpp80) REVERT: I 1357 MET cc_start: 0.9613 (tmm) cc_final: 0.9222 (tmm) REVERT: I 1359 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8812 (pp) REVERT: I 1859 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8015 (pmm) REVERT: I 1959 MET cc_start: 0.4578 (mmp) cc_final: 0.4213 (tpp) REVERT: I 2132 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8806 (tp30) REVERT: K 489 MET cc_start: 0.8884 (tpp) cc_final: 0.8606 (tpp) REVERT: K 506 MET cc_start: 0.9039 (tpp) cc_final: 0.8598 (tpp) REVERT: L 568 MET cc_start: 0.8303 (ppp) cc_final: 0.7967 (ppp) REVERT: M 1357 MET cc_start: 0.9434 (tmm) cc_final: 0.9122 (tmm) REVERT: M 1412 MET cc_start: 0.9229 (mmp) cc_final: 0.8998 (mmp) REVERT: M 1800 GLU cc_start: 0.9522 (OUTLIER) cc_final: 0.9319 (mm-30) REVERT: M 1859 MET cc_start: 0.9457 (mtm) cc_final: 0.9152 (mtm) REVERT: M 1862 TYR cc_start: 0.9008 (t80) cc_final: 0.8354 (t80) REVERT: M 2126 LYS cc_start: 0.9554 (tptp) cc_final: 0.9339 (tppt) outliers start: 65 outliers final: 39 residues processed: 250 average time/residue: 0.2224 time to fit residues: 90.3157 Evaluate side-chains 239 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain I residue 1045 GLN Chi-restraints excluded: chain I residue 1349 ARG Chi-restraints excluded: chain I residue 1359 LEU Chi-restraints excluded: chain I residue 1553 PHE Chi-restraints excluded: chain I residue 1859 MET Chi-restraints excluded: chain I residue 2071 LEU Chi-restraints excluded: chain I residue 2132 GLU Chi-restraints excluded: chain I residue 2154 ASN Chi-restraints excluded: chain I residue 2200 GLN Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain L residue 464 LEU Chi-restraints excluded: chain L residue 474 CYS Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain M residue 1036 GLU Chi-restraints excluded: chain M residue 1282 TYR Chi-restraints excluded: chain M residue 1305 HIS Chi-restraints excluded: chain M residue 1367 GLU Chi-restraints excluded: chain M residue 1537 ASP Chi-restraints excluded: chain M residue 1553 PHE Chi-restraints excluded: chain M residue 1554 ILE Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1800 GLU Chi-restraints excluded: chain M residue 1887 THR Chi-restraints excluded: chain M residue 2071 LEU Chi-restraints excluded: chain M residue 2153 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 41 optimal weight: 7.9990 chunk 321 optimal weight: 8.9990 chunk 387 optimal weight: 2.9990 chunk 255 optimal weight: 8.9990 chunk 429 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 323 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 182 optimal weight: 0.0980 chunk 37 optimal weight: 10.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1045 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1850 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 = 0.3662 r_free = 0.3662 target = 0.054985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.038772 restraints weight = 312319.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.039938 restraints weight = 174247.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.040654 restraints weight = 122564.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.041097 restraints weight = 98963.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.041347 restraints weight = 87097.843| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 36180 Z= 0.289 Angle : 0.737 12.809 49043 Z= 0.384 Chirality : 0.045 0.222 5352 Planarity : 0.005 0.075 6261 Dihedral : 4.965 27.845 4742 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.18 % Favored : 88.73 % Rotamer: Outliers : 1.97 % Allowed : 17.76 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -1.15 (0.13), residues: 4312 helix: 0.45 (0.14), residues: 1443 sheet: -0.38 (0.19), residues: 759 loop : -1.80 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 461 TYR 0.022 0.002 TYR M1157 PHE 0.023 0.002 PHE M1551 TRP 0.022 0.002 TRP I2244 HIS 0.007 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00616 (36117) covalent geometry : angle 0.73494 (48917) SS BOND : bond 0.00542 ( 63) SS BOND : angle 1.38022 ( 126) hydrogen bonds : bond 0.04999 ( 1406) hydrogen bonds : angle 5.12516 ( 4146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 186 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8454 (tptp) REVERT: B 375 TYR cc_start: 0.9467 (t80) cc_final: 0.9204 (t80) REVERT: C 453 ASP cc_start: 0.8905 (m-30) cc_final: 0.8696 (m-30) REVERT: C 530 THR cc_start: 0.9596 (OUTLIER) cc_final: 0.9328 (p) REVERT: C 561 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9194 (mm) REVERT: D 549 GLU cc_start: 0.8423 (pm20) cc_final: 0.8084 (pm20) REVERT: E 499 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8901 (mmmt) REVERT: G 453 ASP cc_start: 0.8935 (t0) cc_final: 0.8585 (t0) REVERT: H 506 MET cc_start: 0.8759 (mmm) cc_final: 0.8496 (mmm) REVERT: H 518 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7261 (m170) REVERT: I 1313 GLU cc_start: 0.9086 (pp20) cc_final: 0.8827 (pp20) REVERT: I 1349 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8420 (mpp80) REVERT: I 1357 MET cc_start: 0.9554 (tmm) cc_final: 0.9145 (tmm) REVERT: I 1359 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8806 (pp) REVERT: I 1859 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8030 (pmm) REVERT: I 1959 MET cc_start: 0.4371 (mmp) cc_final: 0.4015 (tpp) REVERT: I 2132 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.8836 (tp30) REVERT: K 489 MET cc_start: 0.8971 (tpp) cc_final: 0.8697 (tpp) REVERT: K 506 MET cc_start: 0.9082 (tpp) cc_final: 0.8700 (tpp) REVERT: L 568 MET cc_start: 0.8254 (ppp) cc_final: 0.7896 (ppp) REVERT: M 1357 MET cc_start: 0.9398 (tmm) cc_final: 0.9071 (tmm) REVERT: M 1412 MET cc_start: 0.9219 (mmp) cc_final: 0.9002 (mmp) REVERT: M 1783 MET cc_start: 0.6479 (ttt) cc_final: 0.5784 (tpt) REVERT: M 1862 TYR cc_start: 0.9089 (t80) cc_final: 0.8392 (t80) REVERT: M 2126 LYS cc_start: 0.9505 (tptp) cc_final: 0.9266 (tppt) outliers start: 78 outliers final: 55 residues processed: 248 average time/residue: 0.2232 time to fit residues: 90.1101 Evaluate side-chains 243 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain I residue 1349 ARG Chi-restraints excluded: chain I residue 1359 LEU Chi-restraints excluded: chain I residue 1553 PHE Chi-restraints excluded: chain I residue 1859 MET Chi-restraints excluded: chain I residue 2071 LEU Chi-restraints excluded: chain I residue 2081 LEU Chi-restraints excluded: chain I residue 2132 GLU Chi-restraints excluded: chain I residue 2154 ASN Chi-restraints excluded: chain I residue 2200 GLN Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 464 LEU Chi-restraints excluded: chain L residue 474 CYS Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain M residue 1036 GLU Chi-restraints excluded: chain M residue 1121 PHE Chi-restraints excluded: chain M residue 1234 THR Chi-restraints excluded: chain M residue 1282 TYR Chi-restraints excluded: chain M residue 1367 GLU Chi-restraints excluded: chain M residue 1537 ASP Chi-restraints excluded: chain M residue 1553 PHE Chi-restraints excluded: chain M residue 1554 ILE Chi-restraints excluded: chain M residue 1597 TYR Chi-restraints excluded: chain M residue 1603 MET Chi-restraints excluded: chain M residue 1609 TYR Chi-restraints excluded: chain M residue 1654 LEU Chi-restraints excluded: chain M residue 1800 GLU Chi-restraints excluded: chain M residue 1887 THR Chi-restraints excluded: chain M residue 2071 LEU Chi-restraints excluded: chain M residue 2140 LYS Chi-restraints excluded: chain M residue 2153 TRP Chi-restraints excluded: chain M residue 2212 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 280 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 277 optimal weight: 0.9980 chunk 314 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 167 optimal weight: 0.0770 chunk 305 optimal weight: 5.9990 chunk 1 optimal weight: 0.0470 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.056829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.040711 restraints weight = 298976.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.041935 restraints weight = 166043.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.042710 restraints weight = 115831.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.043181 restraints weight = 92697.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.043452 restraints weight = 81134.200| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36180 Z= 0.124 Angle : 0.667 14.792 49043 Z= 0.337 Chirality : 0.044 0.226 5352 Planarity : 0.004 0.078 6261 Dihedral : 4.660 26.645 4742 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.84 % Rotamer: Outliers : 1.36 % Allowed : 19.22 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -0.87 (0.13), residues: 4312 helix: 0.70 (0.14), residues: 1417 sheet: -0.04 (0.19), residues: 750 loop : -1.70 (0.14), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 491 TYR 0.031 0.001 TYR B 534 PHE 0.033 0.001 PHE I2066 TRP 0.024 0.001 TRP M2244 HIS 0.004 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00262 (36117) covalent geometry : angle 0.66514 (48917) SS BOND : bond 0.00490 ( 63) SS BOND : angle 1.14333 ( 126) hydrogen bonds : bond 0.04219 ( 1406) hydrogen bonds : angle 4.75753 ( 4146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 TYR cc_start: 0.9490 (t80) cc_final: 0.9256 (t80) REVERT: C 453 ASP cc_start: 0.8866 (m-30) cc_final: 0.8640 (m-30) REVERT: D 465 ASN cc_start: 0.8904 (m110) cc_final: 0.8476 (m110) REVERT: D 527 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7875 (tp30) REVERT: F 453 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8141 (t0) REVERT: G 453 ASP cc_start: 0.8914 (t0) cc_final: 0.8545 (t0) REVERT: H 489 MET cc_start: 0.7938 (tpp) cc_final: 0.7699 (tpp) REVERT: H 518 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7239 (m170) REVERT: I 1313 GLU cc_start: 0.8950 (pp20) cc_final: 0.8660 (pp20) REVERT: I 1357 MET cc_start: 0.9589 (tmm) cc_final: 0.9188 (tmm) REVERT: I 1359 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8816 (pp) REVERT: I 1647 MET cc_start: 0.7771 (tmm) cc_final: 0.7225 (tmm) REVERT: I 1859 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8111 (pmm) REVERT: I 1959 MET cc_start: 0.4562 (mmp) cc_final: 0.4180 (tpp) REVERT: I 2132 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8751 (tp30) REVERT: K 489 MET cc_start: 0.8940 (tpp) cc_final: 0.8636 (tpp) REVERT: K 506 MET cc_start: 0.8982 (tpp) cc_final: 0.8671 (tpp) REVERT: L 506 MET cc_start: 0.9174 (mmm) cc_final: 0.8909 (mpp) REVERT: L 568 MET cc_start: 0.8138 (ppp) cc_final: 0.7426 (ppp) REVERT: M 1357 MET cc_start: 0.9408 (tmm) cc_final: 0.9103 (tmm) REVERT: M 1412 MET cc_start: 0.9204 (mmp) cc_final: 0.8978 (mmp) REVERT: M 1783 MET cc_start: 0.6285 (ttt) cc_final: 0.5619 (tpt) REVERT: M 1800 GLU cc_start: 0.9518 (OUTLIER) cc_final: 0.9307 (mm-30) REVERT: M 1859 MET cc_start: 0.9407 (mtm) cc_final: 0.9118 (mtm) REVERT: M 1862 TYR cc_start: 0.9022 (t80) cc_final: 0.8303 (t80) REVERT: M 2126 LYS cc_start: 0.9504 (tptp) cc_final: 0.9274 (tppt) REVERT: M 2156 MET cc_start: 0.8948 (mpp) cc_final: 0.8543 (mpp) outliers start: 54 outliers final: 34 residues processed: 241 average time/residue: 0.2447 time to fit residues: 96.0705 Evaluate side-chains 232 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain I residue 1349 ARG Chi-restraints excluded: chain I residue 1359 LEU Chi-restraints excluded: chain I residue 1859 MET Chi-restraints excluded: chain I residue 2071 LEU Chi-restraints excluded: chain I residue 2132 GLU Chi-restraints excluded: chain I residue 2154 ASN Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 464 LEU Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain M residue 1036 GLU Chi-restraints excluded: chain M residue 1282 TYR Chi-restraints excluded: chain M residue 1367 GLU Chi-restraints excluded: chain M residue 1537 ASP Chi-restraints excluded: chain M residue 1553 PHE Chi-restraints excluded: chain M residue 1597 TYR Chi-restraints excluded: chain M residue 1654 LEU Chi-restraints excluded: chain M residue 1800 GLU Chi-restraints excluded: chain M residue 1887 THR Chi-restraints excluded: chain M residue 2071 LEU Chi-restraints excluded: chain M residue 2153 TRP Chi-restraints excluded: chain M residue 2212 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 76 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 298 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 347 optimal weight: 3.9990 chunk 417 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2200 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1850 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 = 0.3680 r_free = 0.3680 target = 0.055722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.039677 restraints weight = 307855.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.041354 restraints weight = 181151.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.041240 restraints weight = 105966.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.041402 restraints weight = 106669.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.041432 restraints weight = 101408.819| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 36180 Z= 0.221 Angle : 0.695 13.985 49043 Z= 0.356 Chirality : 0.044 0.326 5352 Planarity : 0.004 0.093 6261 Dihedral : 4.714 25.994 4742 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.27 % Favored : 89.63 % Rotamer: Outliers : 1.44 % Allowed : 19.37 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -0.94 (0.13), residues: 4312 helix: 0.67 (0.14), residues: 1427 sheet: -0.13 (0.19), residues: 746 loop : -1.74 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 461 TYR 0.017 0.001 TYR F 534 PHE 0.018 0.001 PHE M1551 TRP 0.022 0.002 TRP L 488 HIS 0.005 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00477 (36117) covalent geometry : angle 0.69265 (48917) SS BOND : bond 0.00452 ( 63) SS BOND : angle 1.26508 ( 126) hydrogen bonds : bond 0.04488 ( 1406) hydrogen bonds : angle 4.90619 ( 4146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8453 (tptp) REVERT: B 375 TYR cc_start: 0.9484 (t80) cc_final: 0.9244 (t80) REVERT: B 554 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8721 (tppt) REVERT: C 453 ASP cc_start: 0.8958 (m-30) cc_final: 0.8723 (m-30) REVERT: C 561 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9225 (mm) REVERT: D 465 ASN cc_start: 0.8914 (m110) cc_final: 0.8481 (m110) REVERT: D 527 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8041 (tp30) REVERT: D 549 GLU cc_start: 0.8506 (pm20) cc_final: 0.8281 (pm20) REVERT: F 468 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8331 (tm-30) REVERT: G 453 ASP cc_start: 0.8997 (t0) cc_final: 0.8634 (t0) REVERT: H 489 MET cc_start: 0.8008 (tpp) cc_final: 0.7803 (tpp) REVERT: H 506 MET cc_start: 0.8856 (mmm) cc_final: 0.8492 (mmm) REVERT: H 518 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7286 (m170) REVERT: I 1313 GLU cc_start: 0.9008 (pp20) cc_final: 0.8744 (pp20) REVERT: I 1349 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8432 (mpp80) REVERT: I 1357 MET cc_start: 0.9609 (tmm) cc_final: 0.9206 (tmm) REVERT: I 1359 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8756 (pp) REVERT: I 1647 MET cc_start: 0.7844 (tmm) cc_final: 0.7298 (tmm) REVERT: I 1859 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8130 (pmm) REVERT: I 1959 MET cc_start: 0.4527 (mmp) cc_final: 0.4158 (tpp) REVERT: K 489 MET cc_start: 0.9071 (tpp) cc_final: 0.8793 (tpp) REVERT: K 506 MET cc_start: 0.9140 (tpp) cc_final: 0.8784 (tpp) REVERT: L 568 MET cc_start: 0.8185 (ppp) cc_final: 0.7469 (ppp) REVERT: M 1050 MET cc_start: 0.9033 (mmm) cc_final: 0.8812 (mmm) REVERT: M 1226 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7020 (p90) REVERT: M 1357 MET cc_start: 0.9489 (tmm) cc_final: 0.9155 (tmm) REVERT: M 1412 MET cc_start: 0.9290 (mmp) cc_final: 0.9041 (mmp) REVERT: M 1764 MET cc_start: 0.9257 (ppp) cc_final: 0.8869 (pmm) REVERT: M 1783 MET cc_start: 0.6474 (ttt) cc_final: 0.5101 (tpt) REVERT: M 1859 MET cc_start: 0.9455 (mtm) cc_final: 0.9134 (mtm) REVERT: M 1862 TYR cc_start: 0.9169 (t80) cc_final: 0.8471 (t80) REVERT: M 2126 LYS cc_start: 0.9549 (tptp) cc_final: 0.9323 (tppt) outliers start: 57 outliers final: 43 residues processed: 240 average time/residue: 0.2445 time to fit residues: 95.9628 Evaluate side-chains 238 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain I residue 1349 ARG Chi-restraints excluded: chain I residue 1359 LEU Chi-restraints excluded: chain I residue 1553 PHE Chi-restraints excluded: chain I residue 1859 MET Chi-restraints excluded: chain I residue 2071 LEU Chi-restraints excluded: chain I residue 2154 ASN Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 464 LEU Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 520 ILE Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain M residue 1036 GLU Chi-restraints excluded: chain M residue 1121 PHE Chi-restraints excluded: chain M residue 1226 TYR Chi-restraints excluded: chain M residue 1367 GLU Chi-restraints excluded: chain M residue 1537 ASP Chi-restraints excluded: chain M residue 1553 PHE Chi-restraints excluded: chain M residue 1574 CYS Chi-restraints excluded: chain M residue 1597 TYR Chi-restraints excluded: chain M residue 1654 LEU Chi-restraints excluded: chain M residue 1800 GLU Chi-restraints excluded: chain M residue 1887 THR Chi-restraints excluded: chain M residue 2071 LEU Chi-restraints excluded: chain M residue 2140 LYS Chi-restraints excluded: chain M residue 2153 TRP Chi-restraints excluded: chain M residue 2212 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 242 optimal weight: 9.9990 chunk 348 optimal weight: 0.9990 chunk 254 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 399 optimal weight: 5.9990 chunk 426 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 61 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1043 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1850 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 = 0.3689 r_free = 0.3689 target = 0.056088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.039897 restraints weight = 308513.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.041093 restraints weight = 169451.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.041853 restraints weight = 118666.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.042315 restraints weight = 95282.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.042584 restraints weight = 83541.543| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36180 Z= 0.173 Angle : 0.690 14.678 49043 Z= 0.349 Chirality : 0.044 0.292 5352 Planarity : 0.004 0.079 6261 Dihedral : 4.711 25.740 4742 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.97 % Favored : 89.94 % Rotamer: Outliers : 1.24 % Allowed : 19.82 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -0.92 (0.13), residues: 4312 helix: 0.68 (0.14), residues: 1427 sheet: -0.13 (0.19), residues: 746 loop : -1.73 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 461 TYR 0.035 0.001 TYR B 534 PHE 0.026 0.001 PHE B 358 TRP 0.020 0.001 TRP L 488 HIS 0.004 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00376 (36117) covalent geometry : angle 0.68822 (48917) SS BOND : bond 0.00433 ( 63) SS BOND : angle 1.16923 ( 126) hydrogen bonds : bond 0.04362 ( 1406) hydrogen bonds : angle 4.85771 ( 4146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8421 (tptp) REVERT: B 375 TYR cc_start: 0.9468 (t80) cc_final: 0.9202 (t80) REVERT: C 453 ASP cc_start: 0.8905 (m-30) cc_final: 0.8674 (m-30) REVERT: D 465 ASN cc_start: 0.8906 (m110) cc_final: 0.8478 (m110) REVERT: D 527 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7987 (tp30) REVERT: D 549 GLU cc_start: 0.8485 (pm20) cc_final: 0.8244 (pm20) REVERT: E 461 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8532 (ttp80) REVERT: F 468 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8259 (tm-30) REVERT: G 453 ASP cc_start: 0.8973 (t0) cc_final: 0.8611 (t0) REVERT: H 506 MET cc_start: 0.8804 (mmm) cc_final: 0.8456 (mmm) REVERT: H 518 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7304 (m170) REVERT: I 1313 GLU cc_start: 0.8961 (pp20) cc_final: 0.8702 (pp20) REVERT: I 1349 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8520 (mpp80) REVERT: I 1357 MET cc_start: 0.9580 (tmm) cc_final: 0.9166 (tmm) REVERT: I 1359 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8804 (pp) REVERT: I 1647 MET cc_start: 0.7918 (tmm) cc_final: 0.7402 (tmm) REVERT: I 1859 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8136 (pmm) REVERT: I 1959 MET cc_start: 0.4457 (mmp) cc_final: 0.4124 (tpp) REVERT: K 489 MET cc_start: 0.9062 (tpp) cc_final: 0.8784 (tpp) REVERT: K 506 MET cc_start: 0.9079 (tpp) cc_final: 0.8726 (tpp) REVERT: K 568 MET cc_start: 0.8261 (tmm) cc_final: 0.7698 (tmm) REVERT: L 568 MET cc_start: 0.8133 (ppp) cc_final: 0.7459 (ppp) REVERT: M 1050 MET cc_start: 0.8905 (mmm) cc_final: 0.8696 (mmm) REVERT: M 1226 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6990 (p90) REVERT: M 1357 MET cc_start: 0.9426 (tmm) cc_final: 0.9099 (tmm) REVERT: M 1412 MET cc_start: 0.9232 (mmp) cc_final: 0.9012 (mmp) REVERT: M 1764 MET cc_start: 0.9225 (ppp) cc_final: 0.8830 (pmm) REVERT: M 1783 MET cc_start: 0.6369 (ttt) cc_final: 0.4979 (tpt) REVERT: M 1859 MET cc_start: 0.9436 (mtm) cc_final: 0.8938 (mtm) REVERT: M 1862 TYR cc_start: 0.9108 (t80) cc_final: 0.8397 (t80) REVERT: M 2126 LYS cc_start: 0.9514 (tptp) cc_final: 0.9279 (tppt) outliers start: 49 outliers final: 41 residues processed: 234 average time/residue: 0.2514 time to fit residues: 95.3229 Evaluate side-chains 236 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain I residue 1349 ARG Chi-restraints excluded: chain I residue 1359 LEU Chi-restraints excluded: chain I residue 1553 PHE Chi-restraints excluded: chain I residue 1859 MET Chi-restraints excluded: chain I residue 2071 LEU Chi-restraints excluded: chain I residue 2081 LEU Chi-restraints excluded: chain I residue 2154 ASN Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 464 LEU Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain M residue 1036 GLU Chi-restraints excluded: chain M residue 1121 PHE Chi-restraints excluded: chain M residue 1226 TYR Chi-restraints excluded: chain M residue 1367 GLU Chi-restraints excluded: chain M residue 1537 ASP Chi-restraints excluded: chain M residue 1553 PHE Chi-restraints excluded: chain M residue 1574 CYS Chi-restraints excluded: chain M residue 1597 TYR Chi-restraints excluded: chain M residue 1654 LEU Chi-restraints excluded: chain M residue 1800 GLU Chi-restraints excluded: chain M residue 1887 THR Chi-restraints excluded: chain M residue 2071 LEU Chi-restraints excluded: chain M residue 2153 TRP Chi-restraints excluded: chain M residue 2212 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 297 optimal weight: 3.9990 chunk 122 optimal weight: 0.0570 chunk 15 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 430 optimal weight: 0.0370 chunk 176 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 347 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.056081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.039878 restraints weight = 307020.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.041089 restraints weight = 169911.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.041848 restraints weight = 117770.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.042309 restraints weight = 94633.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.042536 restraints weight = 82993.721| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36180 Z= 0.175 Angle : 0.686 14.645 49043 Z= 0.347 Chirality : 0.044 0.278 5352 Planarity : 0.004 0.086 6261 Dihedral : 4.688 25.397 4742 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.30 % Favored : 89.61 % Rotamer: Outliers : 1.46 % Allowed : 19.77 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.29 % 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 aren not related in a simple way. whole: -0.92 (0.13), residues: 4312 helix: 0.69 (0.14), residues: 1427 sheet: -0.15 (0.19), residues: 750 loop : -1.73 (0.14), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 461 TYR 0.016 0.001 TYR F 534 PHE 0.016 0.001 PHE M1551 TRP 0.020 0.001 TRP L 488 HIS 0.004 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00381 (36117) covalent geometry : angle 0.68414 (48917) SS BOND : bond 0.00441 ( 63) SS BOND : angle 1.16508 ( 126) hydrogen bonds : bond 0.04334 ( 1406) hydrogen bonds : angle 4.84309 ( 4146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8400.77 seconds wall clock time: 145 minutes 47.29 seconds (8747.29 seconds total)