Starting phenix.real_space_refine on Wed Nov 19 06:55:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bpz_7128/11_2025/6bpz_7128.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bpz_7128/11_2025/6bpz_7128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bpz_7128/11_2025/6bpz_7128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bpz_7128/11_2025/6bpz_7128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bpz_7128/11_2025/6bpz_7128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bpz_7128/11_2025/6bpz_7128.map" } resolution = 3.8 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= 0.004 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 111 5.16 5 C 14124 2.51 5 N 3537 2.21 5 O 3681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21453 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1579 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5572 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 670} Chain breaks: 9 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'UNK:plan-1': 59, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1579 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5572 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 670} Chain breaks: 9 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'UNK:plan-1': 59, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1579 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5572 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 670} Chain breaks: 9 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'UNK:plan-1': 59, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 4.79, per 1000 atoms: 0.22 Number of scatterers: 21453 At special positions: 0 Unit cell: (186.43, 174.07, 153.47, 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 111 16.00 O 3681 8.00 N 3537 7.00 C 14124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A2437 " - pdb=" SG CYS A2441 " distance=2.03 Simple disulfide: pdb=" SG CYS B2437 " - pdb=" SG CYS B2441 " distance=2.03 Simple disulfide: pdb=" SG CYS C2437 " - pdb=" SG CYS C2441 " 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: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5202 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 72.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 1150 through 1159 Processing helix chain 'A' and resid 1160 through 1173 removed outlier: 3.530A pdb=" N LEU A1164 " --> pdb=" O TYR A1160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1166 " --> pdb=" O PHE A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1193 removed outlier: 3.616A pdb=" N LEU A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 3.535A pdb=" N LEU A1199 " --> pdb=" O GLY A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1232 removed outlier: 4.148A pdb=" N VAL A1208 " --> pdb=" O ARG A1204 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU A1213 " --> pdb=" O LEU A1209 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1220 " --> pdb=" O TYR A1216 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A1221 " --> pdb=" O ASN A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1298 removed outlier: 3.568A pdb=" N PHE A1289 " --> pdb=" O ILE A1285 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A1290 " --> pdb=" O CYS A1286 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1291 " --> pdb=" O PHE A1287 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A1292 " --> pdb=" O PHE A1288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1307 through 1315 Processing helix chain 'A' and resid 1315 through 1364 removed outlier: 3.734A pdb=" N GLN A1336 " --> pdb=" O ASN A1332 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A1359 " --> pdb=" O LYS A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1415 removed outlier: 3.728A pdb=" N LEU A1414 " --> pdb=" O ASP A1411 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A1415 " --> pdb=" O TYR A1412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1411 through 1415' Processing helix chain 'A' and resid 1502 through 1511 Processing helix chain 'A' and resid 1513 through 1519 removed outlier: 3.589A pdb=" N UNK A1517 " --> pdb=" O UNK A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1619 removed outlier: 4.017A pdb=" N UNK A1607 " --> pdb=" O UNK A1603 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK A1608 " --> pdb=" O UNK A1604 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK A1618 " --> pdb=" O UNK A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1640 removed outlier: 3.773A pdb=" N UNK A1632 " --> pdb=" O UNK A1628 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK A1633 " --> pdb=" O UNK A1629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK A1634 " --> pdb=" O UNK A1630 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK A1635 " --> pdb=" O UNK A1631 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N UNK A1639 " --> pdb=" O UNK A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1667 removed outlier: 4.297A pdb=" N PHE A1665 " --> pdb=" O GLU A1661 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A1666 " --> pdb=" O ALA A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1686 removed outlier: 3.652A pdb=" N ALA A1678 " --> pdb=" O ARG A1674 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS A1686 " --> pdb=" O CYS A1682 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1703 removed outlier: 4.012A pdb=" N ILE A1696 " --> pdb=" O TYR A1692 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS A1699 " --> pdb=" O ILE A1695 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1701 " --> pdb=" O LEU A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1718 removed outlier: 3.509A pdb=" N VAL A1712 " --> pdb=" O LEU A1708 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A1713 " --> pdb=" O VAL A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1747 Processing helix chain 'A' and resid 1783 through 1803 Processing helix chain 'A' and resid 1957 through 1960 Processing helix chain 'A' and resid 1961 through 1967 Processing helix chain 'A' and resid 1976 through 1995 removed outlier: 4.038A pdb=" N ILE A1991 " --> pdb=" O ASP A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2040 Processing helix chain 'A' and resid 2043 through 2063 removed outlier: 4.075A pdb=" N VAL A2055 " --> pdb=" O VAL A2051 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A2056 " --> pdb=" O VAL A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2100 Processing helix chain 'A' and resid 2115 through 2127 removed outlier: 3.599A pdb=" N LEU A2119 " --> pdb=" O ASN A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2142 Processing helix chain 'A' and resid 2148 through 2175 removed outlier: 3.626A pdb=" N TYR A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2184 through 2211 removed outlier: 3.659A pdb=" N LYS A2188 " --> pdb=" O LYS A2184 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A2195 " --> pdb=" O MET A2191 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A2197 " --> pdb=" O GLY A2193 " (cutoff:3.500A) Proline residue: A2206 - end of helix Processing helix chain 'A' and resid 2252 through 2263 Processing helix chain 'A' and resid 2266 through 2274 Processing helix chain 'A' and resid 2275 through 2276 No H-bonds generated for 'chain 'A' and resid 2275 through 2276' Processing helix chain 'A' and resid 2277 through 2279 No H-bonds generated for 'chain 'A' and resid 2277 through 2279' Processing helix chain 'A' and resid 2297 through 2311 Processing helix chain 'A' and resid 2327 through 2330 Processing helix chain 'A' and resid 2348 through 2357 Processing helix chain 'A' and resid 2358 through 2360 No H-bonds generated for 'chain 'A' and resid 2358 through 2360' Processing helix chain 'A' and resid 2467 through 2485 Processing helix chain 'A' and resid 2500 through 2516 Processing helix chain 'A' and resid 2521 through 2533 Processing helix chain 'A' and resid 2535 through 2543 Processing helix chain 'B' and resid 1150 through 1159 Processing helix chain 'B' and resid 1160 through 1173 removed outlier: 3.530A pdb=" N LEU B1164 " --> pdb=" O TYR B1160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B1166 " --> pdb=" O PHE B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1193 removed outlier: 3.615A pdb=" N LEU B1182 " --> pdb=" O SER B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1199 removed outlier: 3.536A pdb=" N LEU B1199 " --> pdb=" O GLY B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1232 removed outlier: 4.149A pdb=" N VAL B1208 " --> pdb=" O ARG B1204 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B1213 " --> pdb=" O LEU B1209 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B1220 " --> pdb=" O TYR B1216 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B1221 " --> pdb=" O ASN B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1298 removed outlier: 3.566A pdb=" N PHE B1289 " --> pdb=" O ILE B1285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B1290 " --> pdb=" O CYS B1286 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B1291 " --> pdb=" O PHE B1287 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B1292 " --> pdb=" O PHE B1288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B1298 " --> pdb=" O ARG B1294 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1306 Processing helix chain 'B' and resid 1307 through 1315 Processing helix chain 'B' and resid 1315 through 1364 removed outlier: 3.734A pdb=" N GLN B1336 " --> pdb=" O ASN B1332 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B1359 " --> pdb=" O LYS B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1415 removed outlier: 3.728A pdb=" N LEU B1414 " --> pdb=" O ASP B1411 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B1415 " --> pdb=" O TYR B1412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1411 through 1415' Processing helix chain 'B' and resid 1502 through 1511 Processing helix chain 'B' and resid 1513 through 1519 removed outlier: 3.589A pdb=" N UNK B1517 " --> pdb=" O UNK B1513 " (cutoff:3.500A) Processing helix chain 'B' and resid 1603 through 1619 removed outlier: 4.017A pdb=" N UNK B1607 " --> pdb=" O UNK B1603 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK B1608 " --> pdb=" O UNK B1604 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK B1618 " --> pdb=" O UNK B1614 " (cutoff:3.500A) Processing helix chain 'B' and resid 1619 through 1640 removed outlier: 3.772A pdb=" N UNK B1632 " --> pdb=" O UNK B1628 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK B1633 " --> pdb=" O UNK B1629 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N UNK B1634 " --> pdb=" O UNK B1630 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK B1635 " --> pdb=" O UNK B1631 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N UNK B1639 " --> pdb=" O UNK B1635 " (cutoff:3.500A) Processing helix chain 'B' and resid 1661 through 1667 removed outlier: 4.296A pdb=" N PHE B1665 " --> pdb=" O GLU B1661 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B1666 " --> pdb=" O ALA B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1672 through 1686 removed outlier: 3.653A pdb=" N ALA B1678 " --> pdb=" O ARG B1674 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS B1686 " --> pdb=" O CYS B1682 " (cutoff:3.500A) Processing helix chain 'B' and resid 1687 through 1703 removed outlier: 4.013A pdb=" N ILE B1696 " --> pdb=" O TYR B1692 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS B1699 " --> pdb=" O ILE B1695 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B1701 " --> pdb=" O LEU B1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1718 removed outlier: 3.509A pdb=" N VAL B1712 " --> pdb=" O LEU B1708 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B1713 " --> pdb=" O VAL B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1726 through 1747 Processing helix chain 'B' and resid 1783 through 1803 Processing helix chain 'B' and resid 1957 through 1960 Processing helix chain 'B' and resid 1961 through 1967 Processing helix chain 'B' and resid 1976 through 1995 removed outlier: 4.038A pdb=" N ILE B1991 " --> pdb=" O ASP B1987 " (cutoff:3.500A) Processing helix chain 'B' and resid 2018 through 2040 Processing helix chain 'B' and resid 2043 through 2063 removed outlier: 4.076A pdb=" N VAL B2055 " --> pdb=" O VAL B2051 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B2056 " --> pdb=" O VAL B2052 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2100 Processing helix chain 'B' and resid 2115 through 2127 removed outlier: 3.599A pdb=" N LEU B2119 " --> pdb=" O ASN B2115 " (cutoff:3.500A) Processing helix chain 'B' and resid 2132 through 2142 Processing helix chain 'B' and resid 2148 through 2175 removed outlier: 3.625A pdb=" N TYR B2175 " --> pdb=" O THR B2171 " (cutoff:3.500A) Processing helix chain 'B' and resid 2184 through 2211 removed outlier: 3.659A pdb=" N LYS B2188 " --> pdb=" O LYS B2184 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B2195 " --> pdb=" O MET B2191 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B2197 " --> pdb=" O GLY B2193 " (cutoff:3.500A) Proline residue: B2206 - end of helix Processing helix chain 'B' and resid 2252 through 2263 Processing helix chain 'B' and resid 2266 through 2274 Processing helix chain 'B' and resid 2275 through 2276 No H-bonds generated for 'chain 'B' and resid 2275 through 2276' Processing helix chain 'B' and resid 2277 through 2279 No H-bonds generated for 'chain 'B' and resid 2277 through 2279' Processing helix chain 'B' and resid 2297 through 2311 Processing helix chain 'B' and resid 2327 through 2330 Processing helix chain 'B' and resid 2348 through 2357 Processing helix chain 'B' and resid 2358 through 2360 No H-bonds generated for 'chain 'B' and resid 2358 through 2360' Processing helix chain 'B' and resid 2467 through 2485 Processing helix chain 'B' and resid 2500 through 2516 Processing helix chain 'B' and resid 2521 through 2533 Processing helix chain 'B' and resid 2535 through 2543 Processing helix chain 'C' and resid 1150 through 1159 Processing helix chain 'C' and resid 1160 through 1173 removed outlier: 3.529A pdb=" N LEU C1164 " --> pdb=" O TYR C1160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C1166 " --> pdb=" O PHE C1162 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1193 removed outlier: 3.615A pdb=" N LEU C1182 " --> pdb=" O SER C1178 " (cutoff:3.500A) Processing helix chain 'C' and resid 1194 through 1199 removed outlier: 3.536A pdb=" N LEU C1199 " --> pdb=" O GLY C1195 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1232 removed outlier: 4.148A pdb=" N VAL C1208 " --> pdb=" O ARG C1204 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU C1213 " --> pdb=" O LEU C1209 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C1220 " --> pdb=" O TYR C1216 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C1221 " --> pdb=" O ASN C1217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1281 through 1298 removed outlier: 3.566A pdb=" N PHE C1289 " --> pdb=" O ILE C1285 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C1290 " --> pdb=" O CYS C1286 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C1291 " --> pdb=" O PHE C1287 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C1292 " --> pdb=" O PHE C1288 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C1298 " --> pdb=" O ARG C1294 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1306 Processing helix chain 'C' and resid 1307 through 1315 Processing helix chain 'C' and resid 1315 through 1364 removed outlier: 3.734A pdb=" N GLN C1336 " --> pdb=" O ASN C1332 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR C1359 " --> pdb=" O LYS C1355 " (cutoff:3.500A) Processing helix chain 'C' and resid 1411 through 1415 removed outlier: 3.728A pdb=" N LEU C1414 " --> pdb=" O ASP C1411 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C1415 " --> pdb=" O TYR C1412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1411 through 1415' Processing helix chain 'C' and resid 1502 through 1511 Processing helix chain 'C' and resid 1513 through 1519 removed outlier: 3.590A pdb=" N UNK C1517 " --> pdb=" O UNK C1513 " (cutoff:3.500A) Processing helix chain 'C' and resid 1603 through 1619 removed outlier: 4.018A pdb=" N UNK C1607 " --> pdb=" O UNK C1603 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK C1608 " --> pdb=" O UNK C1604 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK C1618 " --> pdb=" O UNK C1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 1619 through 1640 removed outlier: 3.772A pdb=" N UNK C1632 " --> pdb=" O UNK C1628 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK C1633 " --> pdb=" O UNK C1629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK C1634 " --> pdb=" O UNK C1630 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK C1635 " --> pdb=" O UNK C1631 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N UNK C1639 " --> pdb=" O UNK C1635 " (cutoff:3.500A) Processing helix chain 'C' and resid 1661 through 1667 removed outlier: 4.297A pdb=" N PHE C1665 " --> pdb=" O GLU C1661 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C1666 " --> pdb=" O ALA C1662 " (cutoff:3.500A) Processing helix chain 'C' and resid 1672 through 1686 removed outlier: 3.652A pdb=" N ALA C1678 " --> pdb=" O ARG C1674 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS C1686 " --> pdb=" O CYS C1682 " (cutoff:3.500A) Processing helix chain 'C' and resid 1687 through 1703 removed outlier: 4.013A pdb=" N ILE C1696 " --> pdb=" O TYR C1692 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS C1699 " --> pdb=" O ILE C1695 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C1701 " --> pdb=" O LEU C1697 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1718 removed outlier: 3.509A pdb=" N VAL C1712 " --> pdb=" O LEU C1708 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU C1713 " --> pdb=" O VAL C1709 " (cutoff:3.500A) Processing helix chain 'C' and resid 1726 through 1747 Processing helix chain 'C' and resid 1783 through 1803 Processing helix chain 'C' and resid 1957 through 1960 Processing helix chain 'C' and resid 1961 through 1967 Processing helix chain 'C' and resid 1976 through 1995 removed outlier: 4.038A pdb=" N ILE C1991 " --> pdb=" O ASP C1987 " (cutoff:3.500A) Processing helix chain 'C' and resid 2018 through 2040 Processing helix chain 'C' and resid 2043 through 2063 removed outlier: 4.076A pdb=" N VAL C2055 " --> pdb=" O VAL C2051 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA C2056 " --> pdb=" O VAL C2052 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2100 Processing helix chain 'C' and resid 2115 through 2127 removed outlier: 3.599A pdb=" N LEU C2119 " --> pdb=" O ASN C2115 " (cutoff:3.500A) Processing helix chain 'C' and resid 2132 through 2142 Processing helix chain 'C' and resid 2148 through 2175 removed outlier: 3.625A pdb=" N TYR C2175 " --> pdb=" O THR C2171 " (cutoff:3.500A) Processing helix chain 'C' and resid 2184 through 2211 removed outlier: 3.659A pdb=" N LYS C2188 " --> pdb=" O LYS C2184 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C2195 " --> pdb=" O MET C2191 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C2197 " --> pdb=" O GLY C2193 " (cutoff:3.500A) Proline residue: C2206 - end of helix Processing helix chain 'C' and resid 2252 through 2263 Processing helix chain 'C' and resid 2266 through 2274 Processing helix chain 'C' and resid 2275 through 2276 No H-bonds generated for 'chain 'C' and resid 2275 through 2276' Processing helix chain 'C' and resid 2277 through 2279 No H-bonds generated for 'chain 'C' and resid 2277 through 2279' Processing helix chain 'C' and resid 2297 through 2311 Processing helix chain 'C' and resid 2327 through 2330 Processing helix chain 'C' and resid 2348 through 2357 Processing helix chain 'C' and resid 2358 through 2360 No H-bonds generated for 'chain 'C' and resid 2358 through 2360' Processing helix chain 'C' and resid 2467 through 2485 Processing helix chain 'C' and resid 2500 through 2516 Processing helix chain 'C' and resid 2521 through 2533 Processing helix chain 'C' and resid 2535 through 2543 Processing sheet with id=AA1, first strand: chain 'A' and resid 2239 through 2243 removed outlier: 3.581A pdb=" N ASP A2225 " --> pdb=" O GLN A2324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2248 through 2250 removed outlier: 3.617A pdb=" N ILE A2286 " --> pdb=" O LEU A2444 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 3.784A pdb=" N HIS A2370 " --> pdb=" O LEU A2399 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU A2399 " --> pdb=" O HIS A2370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2239 through 2243 removed outlier: 3.582A pdb=" N ASP B2225 " --> pdb=" O GLN B2324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2248 through 2250 removed outlier: 3.617A pdb=" N ILE B2286 " --> pdb=" O LEU B2444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2366 through 2372 removed outlier: 3.784A pdb=" N HIS B2370 " --> pdb=" O LEU B2399 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU B2399 " --> pdb=" O HIS B2370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2239 through 2243 removed outlier: 3.581A pdb=" N ASP C2225 " --> pdb=" O GLN C2324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2248 through 2250 removed outlier: 3.617A pdb=" N ILE C2286 " --> pdb=" O LEU C2444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 3.783A pdb=" N HIS C2370 " --> pdb=" O LEU C2399 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU C2399 " --> pdb=" O HIS C2370 " (cutoff:3.500A) 1350 hydrogen bonds defined for protein. 4005 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: 3.71 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5128 1.33 - 1.45: 5024 1.45 - 1.57: 11631 1.57 - 1.69: 0 1.69 - 1.82: 177 Bond restraints: 21960 Sorted by residual: bond pdb=" CG1 ILE B2158 " pdb=" CD1 ILE B2158 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.87e+00 bond pdb=" CG1 ILE A2158 " pdb=" CD1 ILE A2158 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.86e+00 bond pdb=" CG1 ILE C2158 " pdb=" CD1 ILE C2158 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.85e+00 bond pdb=" CB LEU A2443 " pdb=" CG LEU A2443 " ideal model delta sigma weight residual 1.530 1.484 0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" CG1 ILE B1695 " pdb=" CD1 ILE B1695 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.29e+00 ... (remaining 21955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 28977 3.92 - 7.84: 670 7.84 - 11.76: 107 11.76 - 15.69: 24 15.69 - 19.61: 15 Bond angle restraints: 29793 Sorted by residual: angle pdb=" C SER A1148 " pdb=" N TYR A1149 " pdb=" CA TYR A1149 " ideal model delta sigma weight residual 121.54 141.15 -19.61 1.91e+00 2.74e-01 1.05e+02 angle pdb=" C SER C1148 " pdb=" N TYR C1149 " pdb=" CA TYR C1149 " ideal model delta sigma weight residual 121.54 141.12 -19.58 1.91e+00 2.74e-01 1.05e+02 angle pdb=" C SER B1148 " pdb=" N TYR B1149 " pdb=" CA TYR B1149 " ideal model delta sigma weight residual 121.54 141.11 -19.57 1.91e+00 2.74e-01 1.05e+02 angle pdb=" N SER B1148 " pdb=" CA SER B1148 " pdb=" C SER B1148 " ideal model delta sigma weight residual 109.80 121.34 -11.54 1.70e+00 3.46e-01 4.60e+01 angle pdb=" N SER C1148 " pdb=" CA SER C1148 " pdb=" C SER C1148 " ideal model delta sigma weight residual 109.80 121.33 -11.53 1.70e+00 3.46e-01 4.60e+01 ... (remaining 29788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 12079 15.77 - 31.55: 695 31.55 - 47.32: 198 47.32 - 63.09: 12 63.09 - 78.87: 24 Dihedral angle restraints: 13008 sinusoidal: 5034 harmonic: 7974 Sorted by residual: dihedral pdb=" N PHE C2205 " pdb=" C PHE C2205 " pdb=" CA PHE C2205 " pdb=" CB PHE C2205 " ideal model delta harmonic sigma weight residual 122.80 132.69 -9.89 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N PHE A2205 " pdb=" C PHE A2205 " pdb=" CA PHE A2205 " pdb=" CB PHE A2205 " ideal model delta harmonic sigma weight residual 122.80 132.67 -9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N PHE B2205 " pdb=" C PHE B2205 " pdb=" CA PHE B2205 " pdb=" CB PHE B2205 " ideal model delta harmonic sigma weight residual 122.80 132.64 -9.84 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 13005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 3243 0.152 - 0.304: 177 0.304 - 0.456: 6 0.456 - 0.607: 0 0.607 - 0.759: 3 Chirality restraints: 3429 Sorted by residual: chirality pdb=" CG LEU B1805 " pdb=" CB LEU B1805 " pdb=" CD1 LEU B1805 " pdb=" CD2 LEU B1805 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CG LEU A1805 " pdb=" CB LEU A1805 " pdb=" CD1 LEU A1805 " pdb=" CD2 LEU A1805 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CG LEU C1805 " pdb=" CB LEU C1805 " pdb=" CD1 LEU C1805 " pdb=" CD2 LEU C1805 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 3426 not shown) Planarity restraints: 3684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C2542 " 0.034 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP C2542 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C2542 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C2542 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C2542 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C2542 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C2542 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP C2542 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C2542 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C2542 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2542 " -0.033 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP A2542 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP A2542 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A2542 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A2542 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A2542 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A2542 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2542 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2542 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A2542 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B2542 " -0.033 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP B2542 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B2542 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B2542 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B2542 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B2542 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B2542 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B2542 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B2542 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B2542 " -0.008 2.00e-02 2.50e+03 ... (remaining 3681 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5650 2.79 - 3.32: 20717 3.32 - 3.84: 35541 3.84 - 4.37: 40132 4.37 - 4.90: 66407 Nonbonded interactions: 168447 Sorted by model distance: nonbonded pdb=" OH TYR A1970 " pdb=" O ARG A2098 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR B1970 " pdb=" O ARG B2098 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR C1970 " pdb=" O ARG C2098 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A1184 " pdb=" OD1 ASP A1283 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR C1184 " pdb=" OD1 ASP C1283 " model vdw 2.289 3.040 ... (remaining 168442 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.480 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 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 : 0.010 0.116 21963 Z= 0.451 Angle : 1.550 19.608 29799 Z= 0.815 Chirality : 0.078 0.759 3429 Planarity : 0.008 0.079 3684 Dihedral : 11.479 78.869 7797 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.94 % Favored : 91.82 % Rotamer: Outliers : 0.14 % Allowed : 8.42 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.66 (0.12), residues: 2457 helix: -3.15 (0.08), residues: 1581 sheet: -1.14 (0.27), residues: 255 loop : -3.04 (0.21), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG B2502 TYR 0.055 0.005 TYR A2266 PHE 0.047 0.004 PHE C2251 TRP 0.054 0.006 TRP C2542 HIS 0.014 0.004 HIS B1403 Details of bonding type rmsd covalent geometry : bond 0.01018 (21960) covalent geometry : angle 1.55000 (29793) SS BOND : bond 0.00101 ( 3) SS BOND : angle 0.85228 ( 6) hydrogen bonds : bond 0.19923 ( 1350) hydrogen bonds : angle 8.11362 ( 4005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 603 time to evaluate : 0.865 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: symmetry clash revert: symmetry clash REVERT: A 2172 GLU cc_start: 0.7599 (pp20) cc_final: 0.7088 (pp20) REVERT: A 2294 TRP cc_start: 0.6348 (t60) cc_final: 0.6100 (t60) REVERT: B 1743 THR cc_start: 0.8604 (p) cc_final: 0.8003 (m) REVERT: B 2172 GLU cc_start: 0.7686 (pp20) cc_final: 0.7081 (pp20) REVERT: B 2259 LEU cc_start: 0.7160 (tp) cc_final: 0.6921 (tp) REVERT: B 2294 TRP cc_start: 0.6454 (t60) cc_final: 0.6161 (t60) REVERT: B 2503 ILE cc_start: 0.9001 (pp) cc_final: 0.8728 (mt) REVERT: C 1743 THR cc_start: 0.8548 (p) cc_final: 0.7918 (m) REVERT: C 2117 LEU cc_start: 0.8510 (tp) cc_final: 0.8290 (tt) REVERT: C 2172 GLU cc_start: 0.7716 (pp20) cc_final: 0.7140 (pp20) REVERT: C 2503 ILE cc_start: 0.8958 (pp) cc_final: 0.8536 (mt) outliers start: 3 outliers final: 1 residues processed: 606 average time/residue: 0.1459 time to fit residues: 139.2260 Evaluate side-chains 373 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1293 GLN B1293 GLN C1293 GLN C1403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.095245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070876 restraints weight = 81749.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072805 restraints weight = 41292.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.073955 restraints weight = 26270.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.074695 restraints weight = 19989.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075002 restraints weight = 16820.330| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21963 Z= 0.189 Angle : 0.847 11.467 29799 Z= 0.428 Chirality : 0.047 0.222 3429 Planarity : 0.006 0.046 3684 Dihedral : 4.999 33.068 2900 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.28 % Allowed : 14.10 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.15), residues: 2457 helix: -0.70 (0.12), residues: 1590 sheet: -1.00 (0.26), residues: 273 loop : -2.87 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1353 TYR 0.023 0.002 TYR B1785 PHE 0.032 0.002 PHE C1993 TRP 0.021 0.002 TRP B1210 HIS 0.008 0.001 HIS A2370 Details of bonding type rmsd covalent geometry : bond 0.00416 (21960) covalent geometry : angle 0.84682 (29793) SS BOND : bond 0.00350 ( 3) SS BOND : angle 0.87523 ( 6) hydrogen bonds : bond 0.06104 ( 1350) hydrogen bonds : angle 5.35012 ( 4005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 463 time to evaluate : 0.852 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: symmetry clash REVERT: A 1700 MET cc_start: 0.8666 (mtp) cc_final: 0.8283 (mmm) REVERT: A 1744 LYS cc_start: 0.8917 (tmtt) cc_final: 0.8580 (mtpt) REVERT: A 1801 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 2196 ILE cc_start: 0.9073 (pp) cc_final: 0.8754 (mt) REVERT: A 2241 MET cc_start: 0.8918 (tpp) cc_final: 0.7607 (tpp) REVERT: A 2261 GLN cc_start: 0.9524 (mt0) cc_final: 0.9312 (mt0) REVERT: A 2270 MET cc_start: 0.8820 (tmm) cc_final: 0.8269 (mtp) REVERT: A 2272 PHE cc_start: 0.7908 (t80) cc_final: 0.7483 (t80) REVERT: A 2408 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7028 (pm20) REVERT: A 2446 MET cc_start: 0.9216 (ttm) cc_final: 0.8901 (mmm) REVERT: A 2520 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 1801 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8717 (mm) REVERT: B 1988 ILE cc_start: 0.9394 (pt) cc_final: 0.8950 (mt) REVERT: B 2153 MET cc_start: 0.8151 (mtm) cc_final: 0.7031 (mtm) REVERT: B 2222 GLN cc_start: 0.8676 (mp10) cc_final: 0.8305 (mm-40) REVERT: B 2270 MET cc_start: 0.8747 (tmm) cc_final: 0.8161 (mtp) REVERT: B 2408 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7340 (pm20) REVERT: B 2446 MET cc_start: 0.9200 (ttm) cc_final: 0.8832 (mmm) REVERT: B 2485 PHE cc_start: 0.6575 (m-10) cc_final: 0.6252 (m-10) REVERT: B 2503 ILE cc_start: 0.9141 (pp) cc_final: 0.8789 (mt) REVERT: B 2520 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7941 (tm-30) REVERT: C 1736 PHE cc_start: 0.9111 (t80) cc_final: 0.8842 (t80) REVERT: C 1988 ILE cc_start: 0.9381 (pt) cc_final: 0.9061 (mt) REVERT: C 2047 LEU cc_start: 0.9660 (tt) cc_final: 0.9438 (tt) REVERT: C 2196 ILE cc_start: 0.9050 (pp) cc_final: 0.8842 (mt) REVERT: C 2261 GLN cc_start: 0.9552 (mt0) cc_final: 0.9328 (mt0) REVERT: C 2270 MET cc_start: 0.8814 (tmm) cc_final: 0.8249 (mtp) REVERT: C 2272 PHE cc_start: 0.7919 (t80) cc_final: 0.7526 (t80) REVERT: C 2446 MET cc_start: 0.9208 (ttm) cc_final: 0.8825 (mmm) REVERT: C 2503 ILE cc_start: 0.9073 (pp) cc_final: 0.8667 (mt) REVERT: C 2520 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7730 (tm-30) outliers start: 95 outliers final: 42 residues processed: 530 average time/residue: 0.1301 time to fit residues: 112.4306 Evaluate side-chains 416 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 372 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2055 VAL Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2522 GLU Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1794 PHE Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2158 ILE Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2240 THR Chi-restraints excluded: chain B residue 2258 GLU Chi-restraints excluded: chain B residue 2427 LEU Chi-restraints excluded: chain B residue 2532 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1403 HIS Chi-restraints excluded: chain C residue 1801 LEU Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2055 VAL Chi-restraints excluded: chain C residue 2127 LEU Chi-restraints excluded: chain C residue 2158 ILE Chi-restraints excluded: chain C residue 2220 VAL Chi-restraints excluded: chain C residue 2258 GLU Chi-restraints excluded: chain C residue 2427 LEU Chi-restraints excluded: chain C residue 2529 LEU Chi-restraints excluded: chain C residue 2532 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 90 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1348 GLN B1348 GLN C1348 GLN C1403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.094855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070593 restraints weight = 82613.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072506 restraints weight = 41409.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073504 restraints weight = 26653.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074312 restraints weight = 20707.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.074672 restraints weight = 17316.058| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21963 Z= 0.162 Angle : 0.790 11.427 29799 Z= 0.391 Chirality : 0.045 0.230 3429 Planarity : 0.004 0.041 3684 Dihedral : 4.796 30.225 2898 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.64 % Allowed : 16.22 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2457 helix: 0.11 (0.13), residues: 1581 sheet: -0.66 (0.26), residues: 273 loop : -2.67 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1353 TYR 0.026 0.002 TYR B1977 PHE 0.027 0.002 PHE A2125 TRP 0.019 0.002 TRP A2060 HIS 0.016 0.001 HIS C1403 Details of bonding type rmsd covalent geometry : bond 0.00345 (21960) covalent geometry : angle 0.79043 (29793) SS BOND : bond 0.00199 ( 3) SS BOND : angle 0.45618 ( 6) hydrogen bonds : bond 0.05168 ( 1350) hydrogen bonds : angle 4.89264 ( 4005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 414 time to evaluate : 0.880 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1184 TYR cc_start: 0.8092 (m-10) cc_final: 0.7810 (m-10) REVERT: A 1700 MET cc_start: 0.8684 (mtp) cc_final: 0.8301 (mmm) REVERT: A 1801 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8741 (mm) REVERT: A 2153 MET cc_start: 0.8177 (mtm) cc_final: 0.7283 (mtt) REVERT: A 2196 ILE cc_start: 0.8931 (pp) cc_final: 0.8639 (mt) REVERT: A 2261 GLN cc_start: 0.9529 (mt0) cc_final: 0.9282 (mt0) REVERT: A 2270 MET cc_start: 0.8744 (tmm) cc_final: 0.8162 (mtp) REVERT: A 2446 MET cc_start: 0.9227 (ttm) cc_final: 0.8707 (mmt) REVERT: A 2520 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 1170 PHE cc_start: 0.9519 (t80) cc_final: 0.9303 (t80) REVERT: B 1210 TRP cc_start: 0.8421 (t-100) cc_final: 0.8097 (t-100) REVERT: B 1700 MET cc_start: 0.8747 (mtp) cc_final: 0.8522 (mmm) REVERT: B 1797 ARG cc_start: 0.8937 (ttt-90) cc_final: 0.8673 (ttp80) REVERT: B 1801 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 1988 ILE cc_start: 0.9399 (pt) cc_final: 0.9032 (mt) REVERT: B 2241 MET cc_start: 0.9004 (tpp) cc_final: 0.8123 (mmm) REVERT: B 2270 MET cc_start: 0.8958 (tmm) cc_final: 0.8493 (mtp) REVERT: B 2272 PHE cc_start: 0.7829 (t80) cc_final: 0.7567 (t80) REVERT: B 2446 MET cc_start: 0.9217 (ttm) cc_final: 0.8576 (mmt) REVERT: B 2503 ILE cc_start: 0.9103 (pp) cc_final: 0.8822 (mt) REVERT: B 2520 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 1184 TYR cc_start: 0.8149 (m-10) cc_final: 0.7807 (m-10) REVERT: C 1210 TRP cc_start: 0.8444 (t-100) cc_final: 0.8242 (t-100) REVERT: C 1344 GLN cc_start: 0.9006 (pp30) cc_final: 0.8789 (pp30) REVERT: C 1713 LEU cc_start: 0.9495 (tt) cc_final: 0.9290 (tt) REVERT: C 1736 PHE cc_start: 0.9143 (t80) cc_final: 0.8886 (t80) REVERT: C 2147 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9182 (pp) REVERT: C 2196 ILE cc_start: 0.8975 (pp) cc_final: 0.8773 (mt) REVERT: C 2261 GLN cc_start: 0.9527 (mt0) cc_final: 0.9261 (mt0) REVERT: C 2270 MET cc_start: 0.8750 (tmm) cc_final: 0.8181 (mtp) REVERT: C 2272 PHE cc_start: 0.7988 (t80) cc_final: 0.7602 (t80) REVERT: C 2408 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6671 (pm20) REVERT: C 2446 MET cc_start: 0.9252 (ttm) cc_final: 0.8851 (mmm) REVERT: C 2485 PHE cc_start: 0.6556 (m-10) cc_final: 0.6097 (m-10) REVERT: C 2503 ILE cc_start: 0.9040 (pp) cc_final: 0.8720 (mt) REVERT: C 2520 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7658 (tm-30) outliers start: 103 outliers final: 51 residues processed: 497 average time/residue: 0.1291 time to fit residues: 106.4090 Evaluate side-chains 414 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 360 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2220 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2484 PHE Chi-restraints excluded: chain A residue 2497 LEU Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2522 GLU Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1794 PHE Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2240 THR Chi-restraints excluded: chain B residue 2258 GLU Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2484 PHE Chi-restraints excluded: chain B residue 2522 GLU Chi-restraints excluded: chain B residue 2542 TRP Chi-restraints excluded: chain C residue 1166 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1213 LEU Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2147 LEU Chi-restraints excluded: chain C residue 2158 ILE Chi-restraints excluded: chain C residue 2258 GLU Chi-restraints excluded: chain C residue 2427 LEU Chi-restraints excluded: chain C residue 2475 LEU Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2522 GLU Chi-restraints excluded: chain C residue 2529 LEU Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2542 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 83 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.095073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071132 restraints weight = 82826.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072982 restraints weight = 41445.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.074062 restraints weight = 26681.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074847 restraints weight = 20483.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075281 restraints weight = 17140.909| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21963 Z= 0.141 Angle : 0.776 11.501 29799 Z= 0.376 Chirality : 0.044 0.226 3429 Planarity : 0.004 0.043 3684 Dihedral : 4.732 30.740 2898 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.27 % Allowed : 17.03 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2457 helix: 0.43 (0.13), residues: 1578 sheet: -0.50 (0.26), residues: 270 loop : -2.56 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1724 TYR 0.024 0.001 TYR B1977 PHE 0.023 0.002 PHE B2198 TRP 0.016 0.002 TRP C2060 HIS 0.006 0.001 HIS A2490 Details of bonding type rmsd covalent geometry : bond 0.00307 (21960) covalent geometry : angle 0.77600 (29793) SS BOND : bond 0.00212 ( 3) SS BOND : angle 0.46339 ( 6) hydrogen bonds : bond 0.04636 ( 1350) hydrogen bonds : angle 4.61995 ( 4005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 403 time to evaluate : 0.873 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: symmetry clash REVERT: A 1214 ILE cc_start: 0.9479 (mm) cc_final: 0.9270 (pt) REVERT: A 1700 MET cc_start: 0.8671 (mtp) cc_final: 0.8265 (mmm) REVERT: A 1744 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8541 (mtpt) REVERT: A 1801 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8703 (mm) REVERT: A 2153 MET cc_start: 0.8211 (mtm) cc_final: 0.7305 (mtt) REVERT: A 2196 ILE cc_start: 0.8863 (pp) cc_final: 0.8564 (mt) REVERT: A 2261 GLN cc_start: 0.9529 (mt0) cc_final: 0.9317 (mt0) REVERT: A 2270 MET cc_start: 0.8821 (tmm) cc_final: 0.8348 (mtp) REVERT: A 2446 MET cc_start: 0.9203 (ttm) cc_final: 0.8660 (mmt) REVERT: A 2520 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7349 (tm-30) REVERT: B 1170 PHE cc_start: 0.9546 (t80) cc_final: 0.9304 (t80) REVERT: B 1184 TYR cc_start: 0.8066 (m-10) cc_final: 0.7380 (m-10) REVERT: B 1210 TRP cc_start: 0.8419 (t-100) cc_final: 0.8008 (t-100) REVERT: B 1700 MET cc_start: 0.8745 (mtp) cc_final: 0.8378 (mmm) REVERT: B 1713 LEU cc_start: 0.9471 (tt) cc_final: 0.9096 (pp) REVERT: B 1801 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8317 (mm) REVERT: B 1988 ILE cc_start: 0.9356 (pt) cc_final: 0.9101 (mt) REVERT: B 2222 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8319 (mm-40) REVERT: B 2241 MET cc_start: 0.9024 (tpp) cc_final: 0.8180 (mmm) REVERT: B 2270 MET cc_start: 0.8976 (tmm) cc_final: 0.8570 (mtp) REVERT: B 2446 MET cc_start: 0.9238 (ttm) cc_final: 0.8882 (mmm) REVERT: B 2503 ILE cc_start: 0.9075 (pp) cc_final: 0.8834 (mt) REVERT: B 2520 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7689 (tm-30) REVERT: C 1210 TRP cc_start: 0.8414 (t-100) cc_final: 0.8137 (t-100) REVERT: C 1700 MET cc_start: 0.8774 (mmm) cc_final: 0.8265 (mmm) REVERT: C 1736 PHE cc_start: 0.9205 (t80) cc_final: 0.8919 (t80) REVERT: C 1988 ILE cc_start: 0.9326 (pt) cc_final: 0.9038 (mt) REVERT: C 2147 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9170 (pp) REVERT: C 2153 MET cc_start: 0.8115 (mtm) cc_final: 0.7215 (mtm) REVERT: C 2261 GLN cc_start: 0.9548 (mt0) cc_final: 0.9340 (mt0) REVERT: C 2270 MET cc_start: 0.8774 (tmm) cc_final: 0.8193 (mtp) REVERT: C 2272 PHE cc_start: 0.8020 (t80) cc_final: 0.7632 (t80) REVERT: C 2408 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7044 (pm20) REVERT: C 2446 MET cc_start: 0.9274 (ttm) cc_final: 0.8875 (mmm) REVERT: C 2503 ILE cc_start: 0.9058 (pp) cc_final: 0.8790 (mt) REVERT: C 2520 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7379 (tm-30) outliers start: 117 outliers final: 78 residues processed: 492 average time/residue: 0.1292 time to fit residues: 106.3867 Evaluate side-chains 444 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 362 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1336 GLN Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 1993 PHE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2165 ILE Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2220 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2484 PHE Chi-restraints excluded: chain A residue 2497 LEU Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2522 GLU Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1336 GLN Chi-restraints excluded: chain B residue 1709 VAL Chi-restraints excluded: chain B residue 1794 PHE Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1805 LEU Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2165 ILE Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2208 LEU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2222 GLN Chi-restraints excluded: chain B residue 2240 THR Chi-restraints excluded: chain B residue 2258 GLU Chi-restraints excluded: chain B residue 2427 LEU Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2484 PHE Chi-restraints excluded: chain B residue 2497 LEU Chi-restraints excluded: chain B residue 2504 LEU Chi-restraints excluded: chain B residue 2522 GLU Chi-restraints excluded: chain B residue 2529 LEU Chi-restraints excluded: chain B residue 2532 LEU Chi-restraints excluded: chain B residue 2542 TRP Chi-restraints excluded: chain C residue 1166 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1213 LEU Chi-restraints excluded: chain C residue 1309 LEU Chi-restraints excluded: chain C residue 1336 GLN Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1801 LEU Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 1992 ILE Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2147 LEU Chi-restraints excluded: chain C residue 2165 ILE Chi-restraints excluded: chain C residue 2208 LEU Chi-restraints excluded: chain C residue 2240 THR Chi-restraints excluded: chain C residue 2258 GLU Chi-restraints excluded: chain C residue 2427 LEU Chi-restraints excluded: chain C residue 2453 VAL Chi-restraints excluded: chain C residue 2475 LEU Chi-restraints excluded: chain C residue 2484 PHE Chi-restraints excluded: chain C residue 2522 GLU Chi-restraints excluded: chain C residue 2529 LEU Chi-restraints excluded: chain C residue 2542 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 226 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 264 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1217 ASN B1403 HIS C1217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.095017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.070975 restraints weight = 82289.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.072822 restraints weight = 40824.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073948 restraints weight = 26181.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074705 restraints weight = 19903.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.075005 restraints weight = 16804.376| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21963 Z= 0.143 Angle : 0.780 11.840 29799 Z= 0.375 Chirality : 0.045 0.223 3429 Planarity : 0.004 0.043 3684 Dihedral : 4.702 30.481 2898 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.27 % Allowed : 17.39 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2457 helix: 0.66 (0.13), residues: 1575 sheet: -0.35 (0.27), residues: 270 loop : -2.49 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1353 TYR 0.026 0.001 TYR B1216 PHE 0.023 0.002 PHE C1287 TRP 0.014 0.001 TRP B1163 HIS 0.006 0.001 HIS A2490 Details of bonding type rmsd covalent geometry : bond 0.00312 (21960) covalent geometry : angle 0.78055 (29793) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.42802 ( 6) hydrogen bonds : bond 0.04426 ( 1350) hydrogen bonds : angle 4.47450 ( 4005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 399 time to evaluate : 0.877 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: symmetry clash REVERT: A 1184 TYR cc_start: 0.8170 (m-10) cc_final: 0.7834 (m-10) REVERT: A 1700 MET cc_start: 0.8673 (mtp) cc_final: 0.8278 (mmm) REVERT: A 1744 LYS cc_start: 0.8968 (tmtt) cc_final: 0.8585 (mtpt) REVERT: A 1801 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8676 (mm) REVERT: A 1987 ASP cc_start: 0.8715 (t0) cc_final: 0.8462 (t0) REVERT: A 2153 MET cc_start: 0.8164 (mtm) cc_final: 0.7441 (mtt) REVERT: A 2196 ILE cc_start: 0.8828 (pp) cc_final: 0.8546 (mt) REVERT: A 2270 MET cc_start: 0.8871 (tmm) cc_final: 0.8375 (mtp) REVERT: A 2446 MET cc_start: 0.9174 (ttm) cc_final: 0.8660 (mmt) REVERT: A 2485 PHE cc_start: 0.6598 (m-10) cc_final: 0.6298 (m-10) REVERT: A 2503 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8853 (mt) REVERT: A 2520 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 1210 TRP cc_start: 0.8378 (t-100) cc_final: 0.7942 (t-100) REVERT: B 1700 MET cc_start: 0.8716 (mtp) cc_final: 0.8417 (mmm) REVERT: B 1713 LEU cc_start: 0.9479 (tt) cc_final: 0.9088 (pp) REVERT: B 1988 ILE cc_start: 0.9385 (pt) cc_final: 0.9102 (mt) REVERT: B 2023 MET cc_start: 0.8248 (tpp) cc_final: 0.7951 (tpp) REVERT: B 2153 MET cc_start: 0.7966 (mtm) cc_final: 0.7629 (mtm) REVERT: B 2222 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8308 (mm-40) REVERT: B 2270 MET cc_start: 0.8987 (tmm) cc_final: 0.8545 (mtp) REVERT: B 2446 MET cc_start: 0.9224 (ttm) cc_final: 0.8868 (mmm) REVERT: B 2485 PHE cc_start: 0.6449 (m-10) cc_final: 0.5985 (m-10) REVERT: B 2520 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7468 (tm-30) REVERT: C 1210 TRP cc_start: 0.8430 (t-100) cc_final: 0.8128 (t-100) REVERT: C 1700 MET cc_start: 0.8809 (mmm) cc_final: 0.8358 (mmm) REVERT: C 1710 LEU cc_start: 0.9179 (tp) cc_final: 0.8960 (tp) REVERT: C 1713 LEU cc_start: 0.9532 (tt) cc_final: 0.9164 (pp) REVERT: C 1736 PHE cc_start: 0.9196 (t80) cc_final: 0.8898 (t80) REVERT: C 2147 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9190 (pp) REVERT: C 2241 MET cc_start: 0.8990 (tpp) cc_final: 0.8260 (tpp) REVERT: C 2261 GLN cc_start: 0.9561 (mt0) cc_final: 0.9354 (mt0) REVERT: C 2270 MET cc_start: 0.8885 (tmm) cc_final: 0.8354 (mtp) REVERT: C 2272 PHE cc_start: 0.8055 (t80) cc_final: 0.7668 (t80) REVERT: C 2408 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7223 (pm20) REVERT: C 2446 MET cc_start: 0.9260 (ttm) cc_final: 0.8844 (mmm) REVERT: C 2485 PHE cc_start: 0.6519 (m-10) cc_final: 0.5969 (m-10) REVERT: C 2503 ILE cc_start: 0.9050 (pp) cc_final: 0.8837 (mt) REVERT: C 2520 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7515 (tm-30) outliers start: 117 outliers final: 78 residues processed: 489 average time/residue: 0.1216 time to fit residues: 100.9404 Evaluate side-chains 435 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 353 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1336 GLN Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1993 PHE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2055 VAL Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2165 ILE Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2220 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2249 VAL Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2484 PHE Chi-restraints excluded: chain A residue 2497 LEU Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2522 GLU Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1336 GLN Chi-restraints excluded: chain B residue 1709 VAL Chi-restraints excluded: chain B residue 1794 PHE Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1805 LEU Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2165 ILE Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2208 LEU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2222 GLN Chi-restraints excluded: chain B residue 2240 THR Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2484 PHE Chi-restraints excluded: chain B residue 2497 LEU Chi-restraints excluded: chain B residue 2504 LEU Chi-restraints excluded: chain B residue 2522 GLU Chi-restraints excluded: chain B residue 2542 TRP Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1166 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1213 LEU Chi-restraints excluded: chain C residue 1309 LEU Chi-restraints excluded: chain C residue 1336 GLN Chi-restraints excluded: chain C residue 1801 LEU Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 1992 ILE Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2147 LEU Chi-restraints excluded: chain C residue 2165 ILE Chi-restraints excluded: chain C residue 2208 LEU Chi-restraints excluded: chain C residue 2220 VAL Chi-restraints excluded: chain C residue 2240 THR Chi-restraints excluded: chain C residue 2258 GLU Chi-restraints excluded: chain C residue 2427 LEU Chi-restraints excluded: chain C residue 2453 VAL Chi-restraints excluded: chain C residue 2475 LEU Chi-restraints excluded: chain C residue 2484 PHE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2504 LEU Chi-restraints excluded: chain C residue 2522 GLU Chi-restraints excluded: chain C residue 2529 LEU Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2542 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 9 optimal weight: 0.0040 chunk 176 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 240 optimal weight: 0.3980 chunk 81 optimal weight: 8.9990 chunk 228 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.096121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072267 restraints weight = 82465.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074149 restraints weight = 40878.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075318 restraints weight = 26282.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.076048 restraints weight = 20023.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.076472 restraints weight = 16852.500| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21963 Z= 0.129 Angle : 0.784 12.223 29799 Z= 0.370 Chirality : 0.045 0.221 3429 Planarity : 0.004 0.042 3684 Dihedral : 4.621 29.999 2898 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.41 % Allowed : 19.41 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2457 helix: 0.82 (0.13), residues: 1578 sheet: -0.22 (0.27), residues: 270 loop : -2.38 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1674 TYR 0.024 0.001 TYR C1977 PHE 0.026 0.001 PHE B1287 TRP 0.014 0.001 TRP B1163 HIS 0.004 0.001 HIS B2370 Details of bonding type rmsd covalent geometry : bond 0.00270 (21960) covalent geometry : angle 0.78390 (29793) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.40016 ( 6) hydrogen bonds : bond 0.04147 ( 1350) hydrogen bonds : angle 4.29594 ( 4005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 407 time to evaluate : 0.917 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 1356 GLN cc_start: 0.9063 (tp40) cc_final: 0.8834 (tm-30) REVERT: A 1700 MET cc_start: 0.8737 (mtp) cc_final: 0.8295 (mmm) REVERT: A 1801 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8684 (mm) REVERT: A 1977 TYR cc_start: 0.8641 (t80) cc_final: 0.8299 (t80) REVERT: A 2153 MET cc_start: 0.8142 (mtm) cc_final: 0.7303 (mtm) REVERT: A 2196 ILE cc_start: 0.8821 (pp) cc_final: 0.8570 (mt) REVERT: A 2270 MET cc_start: 0.8865 (tmm) cc_final: 0.8400 (mtp) REVERT: A 2446 MET cc_start: 0.9192 (ttm) cc_final: 0.8669 (mmt) REVERT: A 2503 ILE cc_start: 0.9249 (pt) cc_final: 0.8897 (mt) REVERT: A 2520 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7165 (tm-30) REVERT: B 1170 PHE cc_start: 0.9576 (t80) cc_final: 0.9263 (t80) REVERT: B 1184 TYR cc_start: 0.8109 (m-10) cc_final: 0.7587 (m-10) REVERT: B 1700 MET cc_start: 0.8722 (mtp) cc_final: 0.8441 (mmm) REVERT: B 2153 MET cc_start: 0.8050 (mtm) cc_final: 0.7414 (mtm) REVERT: B 2222 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8223 (mm-40) REVERT: B 2446 MET cc_start: 0.9229 (ttm) cc_final: 0.8880 (mmm) REVERT: B 2520 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7239 (tm-30) REVERT: C 1184 TYR cc_start: 0.8053 (m-10) cc_final: 0.7742 (m-10) REVERT: C 1210 TRP cc_start: 0.8491 (t-100) cc_final: 0.8110 (t-100) REVERT: C 1700 MET cc_start: 0.8840 (mmm) cc_final: 0.8396 (mmm) REVERT: C 1710 LEU cc_start: 0.9089 (tp) cc_final: 0.8867 (tt) REVERT: C 1736 PHE cc_start: 0.9195 (t80) cc_final: 0.8899 (t80) REVERT: C 2023 MET cc_start: 0.8396 (tpp) cc_final: 0.8055 (mmt) REVERT: C 2147 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9128 (pp) REVERT: C 2153 MET cc_start: 0.8036 (mtm) cc_final: 0.7109 (mtm) REVERT: C 2172 GLU cc_start: 0.8500 (pp20) cc_final: 0.8138 (pp20) REVERT: C 2241 MET cc_start: 0.8985 (tpp) cc_final: 0.8328 (tpp) REVERT: C 2270 MET cc_start: 0.8867 (tmm) cc_final: 0.8382 (mtp) REVERT: C 2272 PHE cc_start: 0.8061 (t80) cc_final: 0.7678 (t80) REVERT: C 2446 MET cc_start: 0.9299 (ttm) cc_final: 0.8852 (mmm) REVERT: C 2520 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7293 (tm-30) outliers start: 98 outliers final: 71 residues processed: 476 average time/residue: 0.1320 time to fit residues: 106.4451 Evaluate side-chains 433 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 359 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1974 THR Chi-restraints excluded: chain A residue 1993 PHE Chi-restraints excluded: chain A residue 2055 VAL Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2165 ILE Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2220 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2249 VAL Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2484 PHE Chi-restraints excluded: chain A residue 2497 LEU Chi-restraints excluded: chain A residue 2522 GLU Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1709 VAL Chi-restraints excluded: chain B residue 1794 PHE Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1805 LEU Chi-restraints excluded: chain B residue 1974 THR Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2208 LEU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2222 GLN Chi-restraints excluded: chain B residue 2240 THR Chi-restraints excluded: chain B residue 2261 GLN Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2484 PHE Chi-restraints excluded: chain B residue 2497 LEU Chi-restraints excluded: chain B residue 2504 LEU Chi-restraints excluded: chain B residue 2542 TRP Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1166 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1309 LEU Chi-restraints excluded: chain C residue 1801 LEU Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2147 LEU Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2208 LEU Chi-restraints excluded: chain C residue 2220 VAL Chi-restraints excluded: chain C residue 2240 THR Chi-restraints excluded: chain C residue 2258 GLU Chi-restraints excluded: chain C residue 2453 VAL Chi-restraints excluded: chain C residue 2475 LEU Chi-restraints excluded: chain C residue 2484 PHE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2504 LEU Chi-restraints excluded: chain C residue 2522 GLU Chi-restraints excluded: chain C residue 2529 LEU Chi-restraints excluded: chain C residue 2542 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 246 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.093159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068749 restraints weight = 83195.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070521 restraints weight = 42134.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071644 restraints weight = 27399.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072259 restraints weight = 20929.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072727 restraints weight = 17985.073| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21963 Z= 0.206 Angle : 0.822 11.643 29799 Z= 0.401 Chirality : 0.046 0.218 3429 Planarity : 0.004 0.038 3684 Dihedral : 4.700 28.100 2898 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.00 % Allowed : 19.86 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2457 helix: 0.77 (0.13), residues: 1587 sheet: -0.25 (0.28), residues: 270 loop : -2.49 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1674 TYR 0.019 0.002 TYR B1977 PHE 0.037 0.002 PHE C1287 TRP 0.013 0.002 TRP C2429 HIS 0.012 0.001 HIS B2490 Details of bonding type rmsd covalent geometry : bond 0.00471 (21960) covalent geometry : angle 0.82203 (29793) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.38607 ( 6) hydrogen bonds : bond 0.04583 ( 1350) hydrogen bonds : angle 4.51604 ( 4005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 368 time to evaluate : 0.895 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 1356 GLN cc_start: 0.9088 (tp40) cc_final: 0.8832 (tm-30) REVERT: A 1700 MET cc_start: 0.8775 (mtp) cc_final: 0.8217 (mmm) REVERT: A 1801 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8725 (mm) REVERT: A 2080 GLN cc_start: 0.8564 (mm110) cc_final: 0.8305 (mt0) REVERT: A 2153 MET cc_start: 0.8181 (mtm) cc_final: 0.7752 (mtm) REVERT: A 2196 ILE cc_start: 0.8897 (pp) cc_final: 0.8676 (mt) REVERT: A 2446 MET cc_start: 0.9171 (ttm) cc_final: 0.8684 (mmt) REVERT: A 2503 ILE cc_start: 0.9382 (pt) cc_final: 0.9114 (mt) REVERT: A 2520 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 1170 PHE cc_start: 0.9589 (t80) cc_final: 0.9258 (t80) REVERT: B 1700 MET cc_start: 0.8800 (mtp) cc_final: 0.8457 (mmm) REVERT: B 1797 ARG cc_start: 0.9192 (tmt170) cc_final: 0.8811 (tmm160) REVERT: B 2270 MET cc_start: 0.8590 (tpp) cc_final: 0.8201 (ptp) REVERT: B 2446 MET cc_start: 0.9234 (ttm) cc_final: 0.8703 (mmt) REVERT: B 2520 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 1736 PHE cc_start: 0.9234 (t80) cc_final: 0.8963 (t80) REVERT: C 2270 MET cc_start: 0.8874 (tmm) cc_final: 0.8344 (mtp) REVERT: C 2272 PHE cc_start: 0.8188 (t80) cc_final: 0.7822 (t80) REVERT: C 2446 MET cc_start: 0.9276 (ttm) cc_final: 0.8680 (mmt) REVERT: C 2515 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8143 (tm-30) REVERT: C 2520 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7571 (tm-30) outliers start: 111 outliers final: 85 residues processed: 451 average time/residue: 0.1227 time to fit residues: 94.1615 Evaluate side-chains 431 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 345 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1683 VAL Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1993 PHE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2055 VAL Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2158 ILE Chi-restraints excluded: chain A residue 2165 ILE Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2220 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2249 VAL Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2484 PHE Chi-restraints excluded: chain A residue 2497 LEU Chi-restraints excluded: chain A residue 2504 LEU Chi-restraints excluded: chain A residue 2510 ILE Chi-restraints excluded: chain A residue 2522 GLU Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1709 VAL Chi-restraints excluded: chain B residue 1794 PHE Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1805 LEU Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2158 ILE Chi-restraints excluded: chain B residue 2165 ILE Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2208 LEU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2240 THR Chi-restraints excluded: chain B residue 2261 GLN Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2484 PHE Chi-restraints excluded: chain B residue 2497 LEU Chi-restraints excluded: chain B residue 2504 LEU Chi-restraints excluded: chain B residue 2522 GLU Chi-restraints excluded: chain B residue 2542 TRP Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1166 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1309 LEU Chi-restraints excluded: chain C residue 1801 LEU Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2055 VAL Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2147 LEU Chi-restraints excluded: chain C residue 2165 ILE Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2208 LEU Chi-restraints excluded: chain C residue 2220 VAL Chi-restraints excluded: chain C residue 2240 THR Chi-restraints excluded: chain C residue 2258 GLU Chi-restraints excluded: chain C residue 2453 VAL Chi-restraints excluded: chain C residue 2475 LEU Chi-restraints excluded: chain C residue 2484 PHE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2504 LEU Chi-restraints excluded: chain C residue 2510 ILE Chi-restraints excluded: chain C residue 2522 GLU Chi-restraints excluded: chain C residue 2529 LEU Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2542 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 8 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 48 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 244 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.095524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071622 restraints weight = 81837.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073488 restraints weight = 40676.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074656 restraints weight = 26007.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075386 restraints weight = 19765.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075825 restraints weight = 16728.168| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21963 Z= 0.134 Angle : 0.818 12.478 29799 Z= 0.384 Chirality : 0.045 0.212 3429 Planarity : 0.004 0.037 3684 Dihedral : 4.637 28.149 2898 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.60 % Allowed : 22.07 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2457 helix: 0.92 (0.13), residues: 1587 sheet: -0.24 (0.28), residues: 270 loop : -2.42 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1674 TYR 0.019 0.001 TYR C1977 PHE 0.035 0.002 PHE A1287 TRP 0.018 0.002 TRP A1163 HIS 0.004 0.001 HIS A2370 Details of bonding type rmsd covalent geometry : bond 0.00284 (21960) covalent geometry : angle 0.81838 (29793) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.46528 ( 6) hydrogen bonds : bond 0.04106 ( 1350) hydrogen bonds : angle 4.25490 ( 4005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 393 time to evaluate : 0.788 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 1184 TYR cc_start: 0.8047 (m-10) cc_final: 0.7709 (m-10) REVERT: A 1356 GLN cc_start: 0.9023 (tp40) cc_final: 0.8812 (tm-30) REVERT: A 1700 MET cc_start: 0.8682 (mtp) cc_final: 0.8267 (mmm) REVERT: A 1731 MET cc_start: 0.9338 (mmm) cc_final: 0.8886 (mmm) REVERT: A 1801 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8715 (mm) REVERT: A 1977 TYR cc_start: 0.8787 (t80) cc_final: 0.8178 (t80) REVERT: A 2027 GLN cc_start: 0.8986 (tt0) cc_final: 0.8701 (tt0) REVERT: A 2196 ILE cc_start: 0.8875 (pp) cc_final: 0.8641 (mt) REVERT: A 2270 MET cc_start: 0.8484 (tpp) cc_final: 0.8050 (ptp) REVERT: A 2446 MET cc_start: 0.9156 (ttm) cc_final: 0.8695 (mmt) REVERT: A 2503 ILE cc_start: 0.9202 (pt) cc_final: 0.8995 (mt) REVERT: A 2520 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7179 (tm-30) REVERT: B 1170 PHE cc_start: 0.9579 (t80) cc_final: 0.9317 (t80) REVERT: B 1700 MET cc_start: 0.8711 (mtp) cc_final: 0.8283 (mmm) REVERT: B 1797 ARG cc_start: 0.9177 (tmt170) cc_final: 0.8779 (tmm160) REVERT: B 2080 GLN cc_start: 0.8577 (mm110) cc_final: 0.8281 (mt0) REVERT: B 2222 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8149 (mm-40) REVERT: B 2258 GLU cc_start: 0.9352 (mp0) cc_final: 0.9119 (mp0) REVERT: B 2446 MET cc_start: 0.9200 (ttm) cc_final: 0.8644 (mmt) REVERT: B 2520 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7305 (tm-30) REVERT: C 1731 MET cc_start: 0.9326 (mmm) cc_final: 0.9014 (mmm) REVERT: C 1736 PHE cc_start: 0.9173 (t80) cc_final: 0.8803 (t80) REVERT: C 1801 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8643 (mm) REVERT: C 2028 PHE cc_start: 0.9362 (m-10) cc_final: 0.9154 (m-10) REVERT: C 2147 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9214 (pp) REVERT: C 2270 MET cc_start: 0.8818 (tmm) cc_final: 0.8390 (mtp) REVERT: C 2272 PHE cc_start: 0.8089 (t80) cc_final: 0.7699 (t80) REVERT: C 2446 MET cc_start: 0.9289 (ttm) cc_final: 0.8703 (mmt) REVERT: C 2520 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7254 (tm-30) outliers start: 80 outliers final: 60 residues processed: 452 average time/residue: 0.1216 time to fit residues: 93.1951 Evaluate side-chains 419 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 355 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 1993 PHE Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2165 ILE Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2484 PHE Chi-restraints excluded: chain A residue 2522 GLU Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1794 PHE Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1805 LEU Chi-restraints excluded: chain B residue 2158 ILE Chi-restraints excluded: chain B residue 2171 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2208 LEU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2222 GLN Chi-restraints excluded: chain B residue 2240 THR Chi-restraints excluded: chain B residue 2261 GLN Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2484 PHE Chi-restraints excluded: chain B residue 2497 LEU Chi-restraints excluded: chain B residue 2504 LEU Chi-restraints excluded: chain B residue 2522 GLU Chi-restraints excluded: chain B residue 2542 TRP Chi-restraints excluded: chain C residue 1166 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1309 LEU Chi-restraints excluded: chain C residue 1801 LEU Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 2147 LEU Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2208 LEU Chi-restraints excluded: chain C residue 2220 VAL Chi-restraints excluded: chain C residue 2240 THR Chi-restraints excluded: chain C residue 2258 GLU Chi-restraints excluded: chain C residue 2453 VAL Chi-restraints excluded: chain C residue 2484 PHE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2504 LEU Chi-restraints excluded: chain C residue 2522 GLU Chi-restraints excluded: chain C residue 2529 LEU Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2542 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 180 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 151 optimal weight: 0.3980 chunk 179 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.093123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068818 restraints weight = 83193.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070626 restraints weight = 41669.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071752 restraints weight = 26949.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072474 restraints weight = 20491.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072917 restraints weight = 17327.509| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21963 Z= 0.197 Angle : 0.843 13.914 29799 Z= 0.411 Chirality : 0.046 0.208 3429 Planarity : 0.004 0.037 3684 Dihedral : 4.721 25.772 2898 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.14 % Allowed : 21.53 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2457 helix: 0.83 (0.13), residues: 1578 sheet: -0.28 (0.28), residues: 270 loop : -2.47 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1674 TYR 0.018 0.002 TYR A1977 PHE 0.040 0.002 PHE C1287 TRP 0.013 0.002 TRP B2542 HIS 0.010 0.001 HIS B2490 Details of bonding type rmsd covalent geometry : bond 0.00454 (21960) covalent geometry : angle 0.84325 (29793) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.39566 ( 6) hydrogen bonds : bond 0.04503 ( 1350) hydrogen bonds : angle 4.50122 ( 4005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 356 time to evaluate : 0.859 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 1356 GLN cc_start: 0.9063 (tp40) cc_final: 0.8831 (tm-30) REVERT: A 1700 MET cc_start: 0.8727 (mtp) cc_final: 0.8318 (mmm) REVERT: A 1731 MET cc_start: 0.9364 (mmm) cc_final: 0.9009 (mmm) REVERT: A 1801 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8720 (mm) REVERT: A 1805 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8864 (mm) REVERT: A 2196 ILE cc_start: 0.8928 (pp) cc_final: 0.8709 (mt) REVERT: A 2446 MET cc_start: 0.9115 (ttm) cc_final: 0.8694 (mmt) REVERT: A 2503 ILE cc_start: 0.9379 (pt) cc_final: 0.9130 (mt) REVERT: A 2520 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 1170 PHE cc_start: 0.9591 (t80) cc_final: 0.9345 (t80) REVERT: B 1700 MET cc_start: 0.8715 (mtp) cc_final: 0.8228 (mmm) REVERT: B 1731 MET cc_start: 0.9261 (mmm) cc_final: 0.8456 (mpp) REVERT: B 1797 ARG cc_start: 0.9171 (tmt170) cc_final: 0.8795 (tmm160) REVERT: B 2080 GLN cc_start: 0.8579 (mm110) cc_final: 0.8266 (mt0) REVERT: B 2446 MET cc_start: 0.9206 (ttm) cc_final: 0.8708 (mmt) REVERT: B 2520 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 1736 PHE cc_start: 0.9227 (t80) cc_final: 0.8934 (t80) REVERT: C 2158 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9238 (mt) REVERT: C 2270 MET cc_start: 0.8832 (tmm) cc_final: 0.8376 (mtp) REVERT: C 2272 PHE cc_start: 0.8184 (t80) cc_final: 0.7790 (t80) REVERT: C 2446 MET cc_start: 0.9275 (ttm) cc_final: 0.8711 (mmt) REVERT: C 2515 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 2520 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7577 (tm-30) outliers start: 92 outliers final: 82 residues processed: 419 average time/residue: 0.1244 time to fit residues: 88.7270 Evaluate side-chains 430 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 345 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1993 PHE Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2165 ILE Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2220 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2484 PHE Chi-restraints excluded: chain A residue 2497 LEU Chi-restraints excluded: chain A residue 2504 LEU Chi-restraints excluded: chain A residue 2510 ILE Chi-restraints excluded: chain A residue 2522 GLU Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2532 LEU Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1719 MET Chi-restraints excluded: chain B residue 1794 PHE Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1805 LEU Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2138 MET Chi-restraints excluded: chain B residue 2158 ILE Chi-restraints excluded: chain B residue 2165 ILE Chi-restraints excluded: chain B residue 2171 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2207 LEU Chi-restraints excluded: chain B residue 2208 LEU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2240 THR Chi-restraints excluded: chain B residue 2261 GLN Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2484 PHE Chi-restraints excluded: chain B residue 2497 LEU Chi-restraints excluded: chain B residue 2522 GLU Chi-restraints excluded: chain B residue 2532 LEU Chi-restraints excluded: chain B residue 2542 TRP Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1166 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1309 LEU Chi-restraints excluded: chain C residue 1801 LEU Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2055 VAL Chi-restraints excluded: chain C residue 2131 LEU Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2147 LEU Chi-restraints excluded: chain C residue 2158 ILE Chi-restraints excluded: chain C residue 2165 ILE Chi-restraints excluded: chain C residue 2171 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2208 LEU Chi-restraints excluded: chain C residue 2220 VAL Chi-restraints excluded: chain C residue 2240 THR Chi-restraints excluded: chain C residue 2453 VAL Chi-restraints excluded: chain C residue 2475 LEU Chi-restraints excluded: chain C residue 2484 PHE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2504 LEU Chi-restraints excluded: chain C residue 2510 ILE Chi-restraints excluded: chain C residue 2522 GLU Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2542 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 93 optimal weight: 8.9990 chunk 211 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.093084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068868 restraints weight = 83108.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070668 restraints weight = 41652.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071797 restraints weight = 26950.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072488 restraints weight = 20528.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.072841 restraints weight = 17444.860| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21963 Z= 0.183 Angle : 0.869 16.312 29799 Z= 0.416 Chirality : 0.046 0.202 3429 Planarity : 0.004 0.037 3684 Dihedral : 4.767 26.126 2898 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.87 % Allowed : 22.30 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2457 helix: 0.83 (0.13), residues: 1572 sheet: -0.26 (0.29), residues: 270 loop : -2.46 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1674 TYR 0.019 0.001 TYR A1977 PHE 0.041 0.002 PHE A1287 TRP 0.023 0.002 TRP A2060 HIS 0.007 0.001 HIS B2490 Details of bonding type rmsd covalent geometry : bond 0.00421 (21960) covalent geometry : angle 0.86878 (29793) SS BOND : bond 0.00268 ( 3) SS BOND : angle 0.47268 ( 6) hydrogen bonds : bond 0.04496 ( 1350) hydrogen bonds : angle 4.51467 ( 4005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 352 time to evaluate : 0.820 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 1356 GLN cc_start: 0.9057 (tp40) cc_final: 0.8818 (tm-30) REVERT: A 1700 MET cc_start: 0.8795 (mtp) cc_final: 0.8312 (mmm) REVERT: A 1731 MET cc_start: 0.9268 (mmm) cc_final: 0.8931 (mmm) REVERT: A 1801 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8741 (mm) REVERT: A 1805 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8846 (mm) REVERT: A 2023 MET cc_start: 0.8101 (tpp) cc_final: 0.7781 (mmt) REVERT: A 2196 ILE cc_start: 0.8930 (pp) cc_final: 0.8708 (mt) REVERT: A 2446 MET cc_start: 0.9113 (ttm) cc_final: 0.8685 (mmt) REVERT: A 2503 ILE cc_start: 0.9364 (pt) cc_final: 0.9111 (mt) REVERT: A 2520 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 1170 PHE cc_start: 0.9587 (t80) cc_final: 0.9374 (t80) REVERT: B 1700 MET cc_start: 0.8706 (mtp) cc_final: 0.8186 (mmm) REVERT: B 1797 ARG cc_start: 0.9172 (tmt170) cc_final: 0.8795 (tmm160) REVERT: B 2080 GLN cc_start: 0.8577 (mm110) cc_final: 0.8233 (mt0) REVERT: B 2446 MET cc_start: 0.9216 (ttm) cc_final: 0.8693 (mmt) REVERT: B 2520 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7567 (tm-30) REVERT: C 1731 MET cc_start: 0.9297 (mmm) cc_final: 0.8974 (mmm) REVERT: C 1736 PHE cc_start: 0.9186 (t80) cc_final: 0.8869 (t80) REVERT: C 2023 MET cc_start: 0.8610 (mmt) cc_final: 0.8292 (tpp) REVERT: C 2172 GLU cc_start: 0.8602 (pp20) cc_final: 0.8169 (pp20) REVERT: C 2241 MET cc_start: 0.8843 (tpp) cc_final: 0.8386 (mmm) REVERT: C 2270 MET cc_start: 0.8960 (tmm) cc_final: 0.8573 (mtp) REVERT: C 2272 PHE cc_start: 0.8136 (t80) cc_final: 0.7888 (t80) REVERT: C 2446 MET cc_start: 0.9288 (ttm) cc_final: 0.8731 (mmt) REVERT: C 2515 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 2520 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7479 (tm-30) outliers start: 86 outliers final: 76 residues processed: 410 average time/residue: 0.1246 time to fit residues: 87.4028 Evaluate side-chains 420 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 342 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 1993 PHE Chi-restraints excluded: chain A residue 2055 VAL Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2165 ILE Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2208 LEU Chi-restraints excluded: chain A residue 2220 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2453 VAL Chi-restraints excluded: chain A residue 2484 PHE Chi-restraints excluded: chain A residue 2497 LEU Chi-restraints excluded: chain A residue 2504 LEU Chi-restraints excluded: chain A residue 2522 GLU Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2530 ILE Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1177 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1794 PHE Chi-restraints excluded: chain B residue 1800 LEU Chi-restraints excluded: chain B residue 1805 LEU Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2138 MET Chi-restraints excluded: chain B residue 2158 ILE Chi-restraints excluded: chain B residue 2165 ILE Chi-restraints excluded: chain B residue 2171 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2207 LEU Chi-restraints excluded: chain B residue 2208 LEU Chi-restraints excluded: chain B residue 2220 VAL Chi-restraints excluded: chain B residue 2240 THR Chi-restraints excluded: chain B residue 2261 GLN Chi-restraints excluded: chain B residue 2453 VAL Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2484 PHE Chi-restraints excluded: chain B residue 2497 LEU Chi-restraints excluded: chain B residue 2522 GLU Chi-restraints excluded: chain B residue 2532 LEU Chi-restraints excluded: chain B residue 2542 TRP Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1193 LEU Chi-restraints excluded: chain C residue 1309 LEU Chi-restraints excluded: chain C residue 1801 LEU Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 2055 VAL Chi-restraints excluded: chain C residue 2131 LEU Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2147 LEU Chi-restraints excluded: chain C residue 2165 ILE Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2208 LEU Chi-restraints excluded: chain C residue 2220 VAL Chi-restraints excluded: chain C residue 2240 THR Chi-restraints excluded: chain C residue 2453 VAL Chi-restraints excluded: chain C residue 2475 LEU Chi-restraints excluded: chain C residue 2484 PHE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2504 LEU Chi-restraints excluded: chain C residue 2510 ILE Chi-restraints excluded: chain C residue 2522 GLU Chi-restraints excluded: chain C residue 2529 LEU Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2542 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 9 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1344 GLN ** 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 = 0.3640 r_free = 0.3640 target = 0.091833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067445 restraints weight = 82769.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069199 restraints weight = 41769.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070302 restraints weight = 27185.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070979 restraints weight = 20765.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071341 restraints weight = 17725.168| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21963 Z= 0.238 Angle : 0.894 15.723 29799 Z= 0.434 Chirality : 0.048 0.202 3429 Planarity : 0.004 0.037 3684 Dihedral : 4.888 25.146 2898 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.01 % Allowed : 22.39 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2457 helix: 0.80 (0.13), residues: 1554 sheet: -0.39 (0.30), residues: 264 loop : -2.49 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1674 TYR 0.020 0.002 TYR A1977 PHE 0.045 0.002 PHE C1287 TRP 0.023 0.002 TRP A2060 HIS 0.010 0.002 HIS B2490 Details of bonding type rmsd covalent geometry : bond 0.00547 (21960) covalent geometry : angle 0.89450 (29793) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.46357 ( 6) hydrogen bonds : bond 0.04788 ( 1350) hydrogen bonds : angle 4.71961 ( 4005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4521.65 seconds wall clock time: 78 minutes 33.32 seconds (4713.32 seconds total)