Starting phenix.real_space_refine on Mon May 19 08:57:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7h_18216/05_2025/8q7h_18216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7h_18216/05_2025/8q7h_18216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7h_18216/05_2025/8q7h_18216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7h_18216/05_2025/8q7h_18216.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7h_18216/05_2025/8q7h_18216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7h_18216/05_2025/8q7h_18216.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 82 5.16 5 C 11443 2.51 5 N 3321 2.21 5 O 3177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18033 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1403, 8849 Classifications: {'peptide': 1403} Incomplete info: {'truncation_to_alanine': 670} Link IDs: {'PTRANS': 72, 'TRANS': 1330} Chain breaks: 38 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2389 Unresolved non-hydrogen angles: 3037 Unresolved non-hydrogen dihedrals: 1900 Unresolved non-hydrogen chiralities: 213 Planarities with less than four sites: {'GLN:plan1': 59, 'ASP:plan': 46, 'TYR:plan': 11, 'ASN:plan1': 25, 'TRP:plan': 5, 'HIS:plan': 23, 'PHE:plan': 16, 'GLU:plan': 95, 'ARG:plan': 61} Unresolved non-hydrogen planarities: 1434 Chain: "B" Number of atoms: 7047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 7047 Classifications: {'peptide': 1150} Incomplete info: {'truncation_to_alanine': 632} Link IDs: {'PTRANS': 56, 'TRANS': 1093} Chain breaks: 27 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 2307 Unresolved non-hydrogen angles: 2927 Unresolved non-hydrogen dihedrals: 1841 Unresolved non-hydrogen chiralities: 201 Planarities with less than four sites: {'GLN:plan1': 60, 'ASP:plan': 39, 'TYR:plan': 14, 'ASN:plan1': 25, 'TRP:plan': 2, 'HIS:plan': 21, 'PHE:plan': 23, 'GLU:plan': 84, 'ARG:plan': 61} Unresolved non-hydrogen planarities: 1412 Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 578 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "N" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 373 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "E" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 620 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 120} Link IDs: {'TRANS': 124} Chain breaks: 6 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 556 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7255 SG CYS A2088 81.999 46.465 118.922 1.00223.65 S ATOM 7414 SG CYS A2115 78.813 45.120 117.438 1.00227.29 S ATOM 7442 SG CYS A2120 78.661 46.374 121.050 1.00231.17 S ATOM 7204 SG CYS A2070 75.056 34.483 115.440 1.00214.87 S ATOM 7220 SG CYS A2073 73.666 34.737 111.934 1.00220.83 S ATOM 7287 SG CYS A2093 77.190 33.515 112.477 1.00225.15 S ATOM 7303 SG CYS A2096 76.340 37.138 113.078 1.00223.41 S ATOM 7840 SG CYS A2189 77.684 75.750 92.314 1.00151.69 S ATOM 7856 SG CYS A2192 74.045 75.344 93.341 1.00152.98 S ATOM 7927 SG CYS A2203 76.027 78.018 95.089 1.00153.58 S ATOM 7675 SG CYS A2160 82.204 67.510 83.441 1.00150.79 S ATOM 7700 SG CYS A2166 83.554 64.485 81.650 1.00163.13 S ATOM 7789 SG CYS A2181 85.552 67.679 81.730 1.00174.33 S ATOM 7806 SG CYS A2184 82.403 67.491 79.679 1.00175.54 S ATOM 16056 SG CYS C 42 88.483 102.562 90.811 1.00121.30 S ATOM 16072 SG CYS C 45 87.049 101.198 87.332 1.00120.70 S ATOM 16301 SG CYS C 83 85.803 104.386 88.792 1.00142.45 S ATOM 16230 SG CYS C 75 90.922 107.025 102.170 1.00129.34 S ATOM 16381 SG CYS C 94 87.515 105.420 101.069 1.00138.83 S ATOM 16133 SG CYS C 53 85.910 106.581 83.886 1.00136.77 S ATOM 16152 SG CYS C 56 86.552 109.202 81.196 1.00137.77 S ATOM 16182 SG CYS C 68 89.357 108.093 83.741 1.00125.30 S ATOM 17601 SG CYS D 42 77.060 98.377 31.422 1.00160.30 S ATOM 17620 SG CYS D 45 73.425 97.384 30.110 1.00172.92 S ATOM 17842 SG CYS D 83 73.959 98.394 33.648 1.00153.11 S ATOM 17771 SG CYS D 75 87.260 97.394 38.449 1.00107.32 S ATOM 17915 SG CYS D 94 84.743 94.400 38.480 1.00116.28 S ATOM 17661 SG CYS D 53 70.847 100.740 32.789 1.00203.20 S ATOM 17680 SG CYS D 56 68.061 103.224 32.012 1.00222.11 S ATOM 17721 SG CYS D 68 71.831 104.346 32.182 1.00192.27 S Time building chain proxies: 13.63, per 1000 atoms: 0.76 Number of scatterers: 18033 At special positions: 0 Unit cell: (154.918, 212.8, 139.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 82 16.00 O 3177 8.00 N 3321 7.00 C 11443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2601 " pdb="ZN ZN A2601 " - pdb=" ND1 HIS A2090 " pdb="ZN ZN A2601 " - pdb=" SG CYS A2115 " pdb="ZN ZN A2601 " - pdb=" SG CYS A2088 " pdb="ZN ZN A2601 " - pdb=" SG CYS A2120 " pdb=" ZN A2602 " pdb="ZN ZN A2602 " - pdb=" SG CYS A2093 " pdb="ZN ZN A2602 " - pdb=" SG CYS A2073 " pdb="ZN ZN A2602 " - pdb=" SG CYS A2096 " pdb="ZN ZN A2602 " - pdb=" SG CYS A2070 " pdb=" ZN A2603 " pdb="ZN ZN A2603 " - pdb=" NE2 HIS A2198 " pdb="ZN ZN A2603 " - pdb=" SG CYS A2192 " pdb="ZN ZN A2603 " - pdb=" SG CYS A2189 " pdb="ZN ZN A2603 " - pdb=" SG CYS A2203 " pdb=" ZN A2604 " pdb="ZN ZN A2604 " - pdb=" SG CYS A2181 " pdb="ZN ZN A2604 " - pdb=" SG CYS A2160 " pdb="ZN ZN A2604 " - pdb=" SG CYS A2184 " pdb="ZN ZN A2604 " - pdb=" SG CYS A2166 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 80 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 45 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 42 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 83 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 75 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 94 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" ND1 HIS C 82 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 53 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 56 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 68 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" ND1 HIS D 80 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 42 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 45 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 83 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 94 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" ND1 HIS D 82 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 56 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 68 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 53 " Number of angles added : 30 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 15 sheets defined 70.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 135 through 154 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 158 through 165 Processing helix chain 'A' and resid 166 through 176 removed outlier: 4.072A pdb=" N LEU A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.837A pdb=" N ALA A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.620A pdb=" N GLN A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 235 Processing helix chain 'A' and resid 252 through 273 Processing helix chain 'A' and resid 295 through 318 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 510 through 524 Proline residue: A 516 - end of helix Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 566 through 572 removed outlier: 3.803A pdb=" N THR A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 991 Processing helix chain 'A' and resid 992 through 1004 Processing helix chain 'A' and resid 1008 through 1023 Processing helix chain 'A' and resid 1036 through 1044 Processing helix chain 'A' and resid 1050 through 1065 Processing helix chain 'A' and resid 1069 through 1079 Processing helix chain 'A' and resid 1080 through 1091 Processing helix chain 'A' and resid 1099 through 1105 Processing helix chain 'A' and resid 1109 through 1141 Processing helix chain 'A' and resid 1148 through 1158 Processing helix chain 'A' and resid 1303 through 1332 removed outlier: 3.733A pdb=" N GLU A1331 " --> pdb=" O ARG A1327 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A1332 " --> pdb=" O ASP A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1358 Proline residue: A1341 - end of helix removed outlier: 3.528A pdb=" N LEU A1358 " --> pdb=" O ALA A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1384 removed outlier: 3.612A pdb=" N ALA A1364 " --> pdb=" O ASP A1360 " (cutoff:3.500A) Proline residue: A1378 - end of helix Processing helix chain 'A' and resid 1392 through 1406 removed outlier: 3.601A pdb=" N LEU A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A1403 " --> pdb=" O ASP A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1431 removed outlier: 3.786A pdb=" N SER A1417 " --> pdb=" O SER A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1491 Processing helix chain 'A' and resid 1496 through 1517 removed outlier: 3.659A pdb=" N ARG A1500 " --> pdb=" O ASP A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1536 removed outlier: 3.865A pdb=" N MET A1523 " --> pdb=" O ARG A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1563 Processing helix chain 'A' and resid 1566 through 1582 removed outlier: 4.630A pdb=" N GLU A1579 " --> pdb=" O GLN A1575 " (cutoff:3.500A) Proline residue: A1580 - end of helix Processing helix chain 'A' and resid 1583 through 1585 No H-bonds generated for 'chain 'A' and resid 1583 through 1585' Processing helix chain 'A' and resid 1587 through 1608 removed outlier: 4.078A pdb=" N THR A1591 " --> pdb=" O LEU A1587 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS A1595 " --> pdb=" O THR A1591 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A1596 " --> pdb=" O THR A1592 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A1603 " --> pdb=" O HIS A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1612 through 1622 removed outlier: 3.719A pdb=" N ALA A1616 " --> pdb=" O TRP A1612 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A1620 " --> pdb=" O ALA A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1625 No H-bonds generated for 'chain 'A' and resid 1623 through 1625' Processing helix chain 'A' and resid 1628 through 1664 removed outlier: 3.700A pdb=" N LEU A1634 " --> pdb=" O PRO A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1710 No H-bonds generated for 'chain 'A' and resid 1708 through 1710' Processing helix chain 'A' and resid 1721 through 1739 Processing helix chain 'A' and resid 1773 through 1782 removed outlier: 3.873A pdb=" N PHE A1782 " --> pdb=" O LEU A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1798 Processing helix chain 'A' and resid 1800 through 1812 removed outlier: 3.584A pdb=" N LEU A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) Proline residue: A1810 - end of helix Processing helix chain 'A' and resid 1864 through 1882 Processing helix chain 'A' and resid 1890 through 1904 Processing helix chain 'A' and resid 1922 through 1936 Processing helix chain 'A' and resid 1982 through 1988 removed outlier: 3.636A pdb=" N SER A1988 " --> pdb=" O ALA A1984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2017 Processing helix chain 'A' and resid 2021 through 2031 Processing helix chain 'A' and resid 2036 through 2045 Processing helix chain 'A' and resid 2045 through 2053 removed outlier: 4.187A pdb=" N LEU A2049 " --> pdb=" O ASP A2045 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA A2053 " --> pdb=" O LEU A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2107 removed outlier: 3.535A pdb=" N TRP A2097 " --> pdb=" O CYS A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2125 through 2133 Processing helix chain 'A' and resid 2135 through 2154 Processing helix chain 'A' and resid 2202 through 2213 Processing helix chain 'A' and resid 2293 through 2319 Processing helix chain 'A' and resid 2325 through 2352 Processing helix chain 'A' and resid 2364 through 2386 removed outlier: 4.493A pdb=" N GLN A2368 " --> pdb=" O VAL A2364 " (cutoff:3.500A) Processing helix chain 'A' and resid 2392 through 2400 Processing helix chain 'A' and resid 2404 through 2426 Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 110 through 132 removed outlier: 3.784A pdb=" N ARG B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 154 removed outlier: 3.621A pdb=" N ALA B 140 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.721A pdb=" N VAL B 161 " --> pdb=" O PRO B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.967A pdb=" N LEU B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 197 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 252 through 273 Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 319 through 326 removed outlier: 4.252A pdb=" N SER B 324 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU B 325 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 326 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 509 Processing helix chain 'B' and resid 510 through 522 Proline residue: B 516 - end of helix Processing helix chain 'B' and resid 540 through 553 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 567 through 572 Processing helix chain 'B' and resid 983 through 991 Processing helix chain 'B' and resid 991 through 1003 removed outlier: 3.841A pdb=" N PHE B 995 " --> pdb=" O GLU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1024 removed outlier: 4.075A pdb=" N LEU B1012 " --> pdb=" O ASN B1008 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B1024 " --> pdb=" O THR B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1030 removed outlier: 3.514A pdb=" N ALA B1028 " --> pdb=" O PHE B1025 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B1030 " --> pdb=" O GLU B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1043 removed outlier: 3.569A pdb=" N CYS B1040 " --> pdb=" O VAL B1036 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B1041 " --> pdb=" O LEU B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1068 Processing helix chain 'B' and resid 1068 through 1078 Processing helix chain 'B' and resid 1079 through 1087 removed outlier: 4.060A pdb=" N ILE B1083 " --> pdb=" O GLY B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1106 removed outlier: 3.633A pdb=" N ASP B1103 " --> pdb=" O CYS B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1141 removed outlier: 4.202A pdb=" N ARG B1139 " --> pdb=" O GLU B1135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B1140 " --> pdb=" O ASP B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1303 through 1332 removed outlier: 3.818A pdb=" N GLU B1331 " --> pdb=" O ARG B1327 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP B1332 " --> pdb=" O ASP B1328 " (cutoff:3.500A) Processing helix chain 'B' and resid 1335 through 1358 Proline residue: B1341 - end of helix Processing helix chain 'B' and resid 1360 through 1384 removed outlier: 4.478A pdb=" N SER B1377 " --> pdb=" O GLU B1373 " (cutoff:3.500A) Proline residue: B1378 - end of helix Processing helix chain 'B' and resid 1392 through 1405 Processing helix chain 'B' and resid 1413 through 1431 removed outlier: 3.652A pdb=" N SER B1417 " --> pdb=" O SER B1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 1467 through 1491 removed outlier: 4.178A pdb=" N ASN B1471 " --> pdb=" O SER B1467 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B1472 " --> pdb=" O SER B1468 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1517 Processing helix chain 'B' and resid 1519 through 1536 removed outlier: 4.111A pdb=" N MET B1523 " --> pdb=" O ARG B1519 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B1524 " --> pdb=" O ALA B1520 " (cutoff:3.500A) Processing helix chain 'B' and resid 1538 through 1563 Processing helix chain 'B' and resid 1564 through 1577 removed outlier: 3.765A pdb=" N GLY B1572 " --> pdb=" O VAL B1568 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B1573 " --> pdb=" O GLU B1569 " (cutoff:3.500A) Processing helix chain 'B' and resid 1577 through 1582 removed outlier: 3.916A pdb=" N ILE B1581 " --> pdb=" O HIS B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1583 through 1585 No H-bonds generated for 'chain 'B' and resid 1583 through 1585' Processing helix chain 'B' and resid 1589 through 1608 removed outlier: 3.630A pdb=" N HIS B1599 " --> pdb=" O HIS B1595 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B1600 " --> pdb=" O PHE B1596 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP B1603 " --> pdb=" O HIS B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1611 through 1622 removed outlier: 3.979A pdb=" N GLY B1615 " --> pdb=" O SER B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1623 through 1625 No H-bonds generated for 'chain 'B' and resid 1623 through 1625' Processing helix chain 'B' and resid 1628 through 1668 removed outlier: 3.622A pdb=" N LEU B1632 " --> pdb=" O ARG B1628 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B1638 " --> pdb=" O LEU B1634 " (cutoff:3.500A) Processing helix chain 'B' and resid 1715 through 1720 Processing helix chain 'B' and resid 1721 through 1739 removed outlier: 3.581A pdb=" N GLN B1739 " --> pdb=" O TYR B1735 " (cutoff:3.500A) Processing helix chain 'B' and resid 1773 through 1782 Processing helix chain 'B' and resid 1790 through 1798 Processing helix chain 'B' and resid 1800 through 1813 removed outlier: 3.552A pdb=" N LEU B1804 " --> pdb=" O SER B1800 " (cutoff:3.500A) Proline residue: B1810 - end of helix Processing helix chain 'B' and resid 1864 through 1884 Processing helix chain 'B' and resid 1885 through 1887 No H-bonds generated for 'chain 'B' and resid 1885 through 1887' Processing helix chain 'B' and resid 1890 through 1902 removed outlier: 3.860A pdb=" N GLN B1902 " --> pdb=" O LEU B1898 " (cutoff:3.500A) Processing helix chain 'B' and resid 1922 through 1937 Processing helix chain 'B' and resid 2294 through 2316 removed outlier: 3.518A pdb=" N ARG B2316 " --> pdb=" O ASN B2312 " (cutoff:3.500A) Processing helix chain 'B' and resid 2327 through 2354 removed outlier: 3.711A pdb=" N GLN B2341 " --> pdb=" O GLN B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2362 through 2385 Processing helix chain 'B' and resid 2404 through 2430 Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.800A pdb=" N ASN C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'N' and resid 22 through 35 removed outlier: 4.009A pdb=" N LYS N 33 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 18 removed outlier: 3.567A pdb=" N UNK E 9 " --> pdb=" O UNK E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.715A pdb=" N UNK E 104 " --> pdb=" O UNK E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 132 through 146 removed outlier: 4.136A pdb=" N UNK E 136 " --> pdb=" O UNK E 132 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N UNK E 137 " --> pdb=" O UNK E 133 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N UNK E 138 " --> pdb=" O UNK E 134 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N UNK E 141 " --> pdb=" O UNK E 137 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N UNK E 143 " --> pdb=" O UNK E 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 removed outlier: 3.942A pdb=" N ASN D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 6.528A pdb=" N ARG A 41 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 25 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 39 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1695 through 1700 removed outlier: 4.826A pdb=" N VAL C 30 " --> pdb=" O THR A1755 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TRP A1754 " --> pdb=" O LEU A1713 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1695 through 1700 removed outlier: 4.054A pdb=" N GLU C 23 " --> pdb=" O GLN A1763 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU A1761 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TRP C 27 " --> pdb=" O ARG A1759 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG A1759 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A1768 " --> pdb=" O LEU A1846 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1788 through 1789 removed outlier: 3.730A pdb=" N VAL A1788 " --> pdb=" O LEU A1832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1888 through 1889 removed outlier: 3.646A pdb=" N LEU A1888 " --> pdb=" O LEU A1949 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A1949 " --> pdb=" O LEU A1888 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1996 through 1997 Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 7.022A pdb=" N ARG B 41 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU B 25 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 39 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 38 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1696 through 1700 removed outlier: 6.740A pdb=" N SER B1696 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ALA D 31 " --> pdb=" O SER B1696 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B1698 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N TRP D 33 " --> pdb=" O LEU B1698 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU B1700 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU B1761 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP D 27 " --> pdb=" O ARG B1759 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG B1759 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA D 29 " --> pdb=" O LEU B1757 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B1757 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA D 31 " --> pdb=" O THR B1755 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B1755 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TRP D 33 " --> pdb=" O GLN B1753 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLN B1753 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B1768 " --> pdb=" O LEU B1846 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B1848 " --> pdb=" O ILE B1768 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N HIS B1770 " --> pdb=" O LEU B1848 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1788 through 1789 Processing sheet with id=AB1, first strand: chain 'B' and resid 1888 through 1889 removed outlier: 3.981A pdb=" N LEU B1888 " --> pdb=" O LEU B1949 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 70 through 72 Processing sheet with id=AB3, first strand: chain 'N' and resid 2 through 6 Processing sheet with id=AB4, first strand: chain 'N' and resid 48 through 49 Processing sheet with id=AB5, first strand: chain 'E' and resid 22 through 27 removed outlier: 4.726A pdb=" N UNK E 25 " --> pdb=" O UNK E 36 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N UNK E 36 " --> pdb=" O UNK E 25 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N UNK E 27 " --> pdb=" O UNK E 34 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N UNK E 34 " --> pdb=" O UNK E 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 70 through 72 1462 hydrogen bonds defined for protein. 4338 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: 7.87 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6184 1.34 - 1.47: 4388 1.47 - 1.59: 7641 1.59 - 1.72: 0 1.72 - 1.84: 101 Bond restraints: 18314 Sorted by residual: bond pdb=" CA VAL A1809 " pdb=" CB VAL A1809 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.13e+00 bond pdb=" C MET B1633 " pdb=" O MET B1633 " ideal model delta sigma weight residual 1.236 1.255 -0.018 1.15e-02 7.56e+03 2.48e+00 bond pdb=" C GLU A 498 " pdb=" N TRP A 499 " ideal model delta sigma weight residual 1.334 1.316 0.019 1.27e-02 6.20e+03 2.13e+00 bond pdb=" C LEU B1336 " pdb=" O LEU B1336 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.25e-02 6.40e+03 1.43e+00 bond pdb=" C LEU A1336 " pdb=" O LEU A1336 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.26e-02 6.30e+03 1.43e+00 ... (remaining 18309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 24539 1.55 - 3.10: 523 3.10 - 4.64: 103 4.64 - 6.19: 25 6.19 - 7.74: 5 Bond angle restraints: 25195 Sorted by residual: angle pdb=" O GLU A 498 " pdb=" C GLU A 498 " pdb=" N TRP A 499 " ideal model delta sigma weight residual 122.07 125.76 -3.69 1.03e+00 9.43e-01 1.28e+01 angle pdb=" CA GLU A 498 " pdb=" C GLU A 498 " pdb=" N TRP A 499 " ideal model delta sigma weight residual 117.07 113.67 3.40 1.14e+00 7.69e-01 8.89e+00 angle pdb=" C ASP A1387 " pdb=" N ALA A1388 " pdb=" CA ALA A1388 " ideal model delta sigma weight residual 120.38 123.54 -3.16 1.46e+00 4.69e-01 4.67e+00 angle pdb=" C HIS A2198 " pdb=" N TYR A2199 " pdb=" CA TYR A2199 " ideal model delta sigma weight residual 119.83 117.49 2.34 1.11e+00 8.12e-01 4.45e+00 angle pdb=" N VAL A1498 " pdb=" CA VAL A1498 " pdb=" C VAL A1498 " ideal model delta sigma weight residual 108.88 113.41 -4.53 2.16e+00 2.14e-01 4.41e+00 ... (remaining 25190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 9982 18.04 - 36.07: 529 36.07 - 54.11: 94 54.11 - 72.15: 13 72.15 - 90.19: 8 Dihedral angle restraints: 10626 sinusoidal: 2187 harmonic: 8439 Sorted by residual: dihedral pdb=" CA TRP C 35 " pdb=" C TRP C 35 " pdb=" N ASP C 36 " pdb=" CA ASP C 36 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA LEU B1888 " pdb=" C LEU B1888 " pdb=" N HIS B1889 " pdb=" CA HIS B1889 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO A2046 " pdb=" C PRO A2046 " pdb=" N GLU A2047 " pdb=" CA GLU A2047 " ideal model delta harmonic sigma weight residual -180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 10623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2237 0.036 - 0.072: 682 0.072 - 0.108: 188 0.108 - 0.144: 38 0.144 - 0.180: 6 Chirality restraints: 3151 Sorted by residual: chirality pdb=" CB ILE D 44 " pdb=" CA ILE D 44 " pdb=" CG1 ILE D 44 " pdb=" CG2 ILE D 44 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA SER A1377 " pdb=" N SER A1377 " pdb=" C SER A1377 " pdb=" CB SER A1377 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CB ILE C 54 " pdb=" CA ILE C 54 " pdb=" CG1 ILE C 54 " pdb=" CG2 ILE C 54 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 3148 not shown) Planarity restraints: 3295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B1809 " 0.040 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO B1810 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B1810 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B1810 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B1579 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO B1580 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B1580 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B1580 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B1410 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO B1411 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B1411 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1411 " -0.029 5.00e-02 4.00e+02 ... (remaining 3292 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 66 2.55 - 3.14: 15004 3.14 - 3.73: 28527 3.73 - 4.31: 31833 4.31 - 4.90: 52998 Nonbonded interactions: 128428 Sorted by model distance: nonbonded pdb=" OD2 ASP D 97 " pdb="ZN ZN D 202 " model vdw 1.968 2.230 nonbonded pdb=" OD2 ASP C 97 " pdb="ZN ZN C 202 " model vdw 1.986 2.230 nonbonded pdb=" OG SER A 336 " pdb=" OH TYR A 480 " model vdw 2.220 3.040 nonbonded pdb=" NH2 ARG A2414 " pdb=" O GLN C 57 " model vdw 2.225 3.120 nonbonded pdb=" NE2 GLN B1598 " pdb=" O CYS B1704 " model vdw 2.228 3.120 ... (remaining 128423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 21 through 36 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 through 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 53 through 56 or (res \ id 57 through 67 and (name N or name CA or name C or name O or name CB )) or res \ id 68 through 84 or (resid 85 through 86 and (name N or name CA or name C or nam \ e O or name CB )) or resid 87 through 90 or (resid 91 through 92 and (name N or \ name CA or name C or name O or name CB )) or resid 93 through 98 or (resid 99 th \ rough 100 and (name N or name CA or name C or name O or name CB )) or resid 101 \ through 106 or resid 201 through 203)) selection = (chain 'D' and (resid 21 through 29 or (resid 30 through 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 43 or (resid 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 59 or resi \ d 67 through 73 or (resid 74 and (name N or name CA or name C or name O or name \ CB )) or resid 75 through 105 or (resid 106 and (name N or name CA or name C or \ name O or name CB )) or resid 201 through 203)) } 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: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 50.190 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.005 0.277 18353 Z= 0.238 Angle : 0.606 8.188 25225 Z= 0.328 Chirality : 0.039 0.180 3151 Planarity : 0.005 0.061 3295 Dihedral : 12.554 90.187 5064 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2642 helix: 1.41 (0.12), residues: 1778 sheet: -1.63 (0.51), residues: 95 loop : -1.75 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 33 HIS 0.007 0.001 HIS D 80 PHE 0.022 0.001 PHE B1650 TYR 0.019 0.001 TYR B1501 ARG 0.011 0.001 ARG B1424 Details of bonding type rmsd hydrogen bonds : bond 0.11168 ( 1457) hydrogen bonds : angle 5.49183 ( 4338) metal coordination : bond 0.06666 ( 38) metal coordination : angle 3.30153 ( 30) covalent geometry : bond 0.00388 (18314) covalent geometry : angle 0.59535 (25195) Misc. bond : bond 0.09655 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: A 1365 GLN cc_start: 0.8098 (mp10) cc_final: 0.7619 (mp10) REVERT: A 1492 TRP cc_start: 0.8156 (p-90) cc_final: 0.7821 (p-90) REVERT: A 1653 GLN cc_start: 0.7486 (tm-30) cc_final: 0.7100 (tm-30) REVERT: A 1847 TRP cc_start: 0.7320 (t60) cc_final: 0.7068 (t60) REVERT: A 1879 ILE cc_start: 0.7620 (mm) cc_final: 0.7372 (mt) REVERT: B 1318 TYR cc_start: 0.8021 (m-10) cc_final: 0.7588 (m-10) REVERT: B 1321 ARG cc_start: 0.7847 (tpt-90) cc_final: 0.7555 (tpp80) REVERT: B 1347 LEU cc_start: 0.8614 (mp) cc_final: 0.8389 (mt) REVERT: B 1371 CYS cc_start: 0.7838 (t) cc_final: 0.7499 (t) REVERT: B 1472 ILE cc_start: 0.8410 (mt) cc_final: 0.8145 (mm) REVERT: B 1492 TRP cc_start: 0.8522 (p-90) cc_final: 0.7981 (p-90) REVERT: B 1558 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7972 (tp40) REVERT: B 1805 LEU cc_start: 0.8891 (tt) cc_final: 0.8690 (tt) REVERT: B 1850 PRO cc_start: 0.8532 (Cg_exo) cc_final: 0.8245 (Cg_endo) REVERT: B 1927 LEU cc_start: 0.8573 (mm) cc_final: 0.8292 (mp) REVERT: D 81 PHE cc_start: 0.8064 (t80) cc_final: 0.7814 (t80) REVERT: D 101 TRP cc_start: 0.8435 (t-100) cc_final: 0.7985 (t-100) REVERT: D 103 PHE cc_start: 0.8111 (m-80) cc_final: 0.7881 (m-10) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.2691 time to fit residues: 176.4928 Evaluate side-chains 399 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 168 optimal weight: 0.1980 chunk 262 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A1856 ASN ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2380 GLN B1137 HIS B1575 GLN ** B1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN D 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.118258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087707 restraints weight = 45446.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089993 restraints weight = 28461.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.091526 restraints weight = 20289.559| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18353 Z= 0.154 Angle : 0.531 7.487 25225 Z= 0.277 Chirality : 0.037 0.154 3151 Planarity : 0.005 0.060 3295 Dihedral : 3.983 20.641 2930 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2642 helix: 2.32 (0.12), residues: 1816 sheet: -1.74 (0.49), residues: 98 loop : -1.62 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 33 HIS 0.011 0.001 HIS B1137 PHE 0.025 0.002 PHE A1522 TYR 0.015 0.001 TYR B1501 ARG 0.007 0.000 ARG B1421 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 1457) hydrogen bonds : angle 4.36367 ( 4338) metal coordination : bond 0.01458 ( 38) metal coordination : angle 3.00290 ( 30) covalent geometry : bond 0.00297 (18314) covalent geometry : angle 0.52130 (25195) Misc. bond : bond 0.00128 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 480 TYR cc_start: 0.8136 (p90) cc_final: 0.7895 (p90) REVERT: A 543 MET cc_start: 0.8338 (tpt) cc_final: 0.8070 (tpt) REVERT: A 1350 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7243 (mm-30) REVERT: A 1365 GLN cc_start: 0.8087 (mp10) cc_final: 0.7511 (mp10) REVERT: A 1492 TRP cc_start: 0.8039 (p-90) cc_final: 0.7787 (p-90) REVERT: A 1562 ILE cc_start: 0.8052 (tp) cc_final: 0.7809 (tp) REVERT: A 1627 ASN cc_start: 0.8015 (m110) cc_final: 0.7769 (m110) REVERT: A 1653 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 1847 TRP cc_start: 0.7460 (t60) cc_final: 0.7194 (t60) REVERT: A 1879 ILE cc_start: 0.7647 (mm) cc_final: 0.7357 (mt) REVERT: B 1318 TYR cc_start: 0.8040 (m-10) cc_final: 0.7705 (m-10) REVERT: B 1332 ASP cc_start: 0.8718 (t0) cc_final: 0.8456 (t70) REVERT: B 1372 TRP cc_start: 0.8127 (t-100) cc_final: 0.7775 (t-100) REVERT: B 1392 SER cc_start: 0.8174 (p) cc_final: 0.7934 (p) REVERT: B 1421 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7126 (mtm-85) REVERT: B 1472 ILE cc_start: 0.8271 (mt) cc_final: 0.8048 (mm) REVERT: B 1475 CYS cc_start: 0.8125 (t) cc_final: 0.7916 (t) REVERT: B 1492 TRP cc_start: 0.8560 (p-90) cc_final: 0.7948 (p-90) REVERT: B 1510 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7763 (ttm-80) REVERT: B 1704 CYS cc_start: 0.8292 (m) cc_final: 0.7992 (m) REVERT: B 1728 LEU cc_start: 0.8780 (mp) cc_final: 0.8501 (mp) REVERT: B 1759 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7307 (ptm160) REVERT: B 1850 PRO cc_start: 0.8518 (Cg_exo) cc_final: 0.8277 (Cg_endo) REVERT: B 1874 CYS cc_start: 0.7762 (p) cc_final: 0.7546 (p) REVERT: B 1893 LEU cc_start: 0.8956 (tp) cc_final: 0.8753 (tp) REVERT: D 33 TRP cc_start: 0.7666 (p-90) cc_final: 0.7460 (p-90) REVERT: D 81 PHE cc_start: 0.8036 (t80) cc_final: 0.7832 (t80) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.2750 time to fit residues: 174.8885 Evaluate side-chains 390 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 245 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 269 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 145 optimal weight: 0.0370 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 HIS A1870 ASN A1889 HIS ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2380 GLN B1137 HIS B1598 GLN B1644 GLN D 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.118657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.088125 restraints weight = 45290.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.090540 restraints weight = 27651.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.092127 restraints weight = 19305.683| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18353 Z= 0.145 Angle : 0.516 7.756 25225 Z= 0.265 Chirality : 0.037 0.168 3151 Planarity : 0.004 0.050 3295 Dihedral : 3.765 18.180 2930 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.17), residues: 2642 helix: 2.62 (0.12), residues: 1820 sheet: -1.63 (0.50), residues: 98 loop : -1.49 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A1612 HIS 0.010 0.001 HIS B1137 PHE 0.020 0.001 PHE B1650 TYR 0.012 0.001 TYR A1501 ARG 0.006 0.001 ARG B1424 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 1457) hydrogen bonds : angle 4.14780 ( 4338) metal coordination : bond 0.01347 ( 38) metal coordination : angle 2.79060 ( 30) covalent geometry : bond 0.00279 (18314) covalent geometry : angle 0.50691 (25195) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 TYR cc_start: 0.8131 (p90) cc_final: 0.7848 (p90) REVERT: A 543 MET cc_start: 0.8356 (tpt) cc_final: 0.8076 (tpt) REVERT: A 1350 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7228 (mm-30) REVERT: A 1474 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7543 (tm-30) REVERT: A 1492 TRP cc_start: 0.8099 (p-90) cc_final: 0.7813 (p-90) REVERT: A 1562 ILE cc_start: 0.8011 (tp) cc_final: 0.7798 (tp) REVERT: A 1582 MET cc_start: 0.7663 (mtt) cc_final: 0.7431 (mtt) REVERT: A 1627 ASN cc_start: 0.8069 (m110) cc_final: 0.7850 (m110) REVERT: A 1653 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 1847 TRP cc_start: 0.7421 (t60) cc_final: 0.6973 (t60) REVERT: A 1876 LEU cc_start: 0.8872 (mt) cc_final: 0.8554 (mt) REVERT: A 1879 ILE cc_start: 0.7667 (mm) cc_final: 0.7338 (mt) REVERT: B 1332 ASP cc_start: 0.8695 (t0) cc_final: 0.8429 (t70) REVERT: B 1348 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7680 (ttm-80) REVERT: B 1372 TRP cc_start: 0.8175 (t-100) cc_final: 0.7770 (t-100) REVERT: B 1392 SER cc_start: 0.8141 (p) cc_final: 0.7894 (p) REVERT: B 1421 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7088 (mtm-85) REVERT: B 1472 ILE cc_start: 0.8303 (mt) cc_final: 0.8053 (mm) REVERT: B 1475 CYS cc_start: 0.8112 (t) cc_final: 0.7882 (t) REVERT: B 1492 TRP cc_start: 0.8572 (p-90) cc_final: 0.7915 (p-90) REVERT: B 1510 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7766 (ttm-80) REVERT: B 1704 CYS cc_start: 0.8251 (m) cc_final: 0.8009 (m) REVERT: B 1711 CYS cc_start: 0.8096 (m) cc_final: 0.7449 (p) REVERT: B 1759 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7212 (ptm160) REVERT: B 1850 PRO cc_start: 0.8499 (Cg_exo) cc_final: 0.8262 (Cg_endo) REVERT: B 1874 CYS cc_start: 0.7824 (p) cc_final: 0.7592 (p) REVERT: D 33 TRP cc_start: 0.7838 (p-90) cc_final: 0.7573 (p-90) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.2885 time to fit residues: 182.4994 Evaluate side-chains 391 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 139 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A1349 HIS ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2205 HIS B1137 HIS B1644 GLN D 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.116626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.086317 restraints weight = 45503.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.089279 restraints weight = 29895.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.089955 restraints weight = 18365.961| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18353 Z= 0.242 Angle : 0.573 9.027 25225 Z= 0.307 Chirality : 0.039 0.186 3151 Planarity : 0.005 0.054 3295 Dihedral : 4.056 21.026 2930 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.17), residues: 2642 helix: 2.38 (0.12), residues: 1819 sheet: -1.75 (0.48), residues: 98 loop : -1.51 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 42 HIS 0.007 0.001 HIS A1507 PHE 0.025 0.002 PHE A1593 TYR 0.017 0.002 TYR B1111 ARG 0.008 0.001 ARG B1486 Details of bonding type rmsd hydrogen bonds : bond 0.06011 ( 1457) hydrogen bonds : angle 4.48809 ( 4338) metal coordination : bond 0.01617 ( 38) metal coordination : angle 3.49869 ( 30) covalent geometry : bond 0.00461 (18314) covalent geometry : angle 0.56045 (25195) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.747 Fit side-chains REVERT: A 476 TYR cc_start: 0.8048 (m-80) cc_final: 0.7384 (m-80) REVERT: A 480 TYR cc_start: 0.8194 (p90) cc_final: 0.7860 (p90) REVERT: A 543 MET cc_start: 0.8397 (tpt) cc_final: 0.8097 (tpt) REVERT: A 1350 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7402 (mm-30) REVERT: A 1474 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7583 (tm-30) REVERT: A 1492 TRP cc_start: 0.8192 (p-90) cc_final: 0.7856 (p-90) REVERT: A 1582 MET cc_start: 0.7775 (mtt) cc_final: 0.7469 (mtt) REVERT: A 1652 LEU cc_start: 0.8270 (mt) cc_final: 0.8032 (mm) REVERT: A 1653 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 1879 ILE cc_start: 0.7660 (mm) cc_final: 0.7297 (mt) REVERT: A 2414 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7255 (mmm-85) REVERT: B 1332 ASP cc_start: 0.8665 (t0) cc_final: 0.8416 (t70) REVERT: B 1343 LEU cc_start: 0.8873 (mt) cc_final: 0.8669 (mp) REVERT: B 1372 TRP cc_start: 0.8180 (t-100) cc_final: 0.7812 (t-100) REVERT: B 1392 SER cc_start: 0.8121 (p) cc_final: 0.7875 (p) REVERT: B 1424 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7364 (mtm-85) REVERT: B 1469 LEU cc_start: 0.8175 (mt) cc_final: 0.7971 (mm) REVERT: B 1475 CYS cc_start: 0.8149 (t) cc_final: 0.7910 (t) REVERT: B 1510 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7786 (ttm-80) REVERT: B 1582 MET cc_start: 0.7899 (mtp) cc_final: 0.7653 (mtp) REVERT: B 1704 CYS cc_start: 0.8334 (m) cc_final: 0.8055 (m) REVERT: B 1728 LEU cc_start: 0.8781 (mp) cc_final: 0.8504 (mp) REVERT: B 1759 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7232 (ptm160) REVERT: B 1779 LEU cc_start: 0.7976 (mt) cc_final: 0.7746 (mm) REVERT: B 1850 PRO cc_start: 0.8526 (Cg_exo) cc_final: 0.8297 (Cg_endo) REVERT: B 1874 CYS cc_start: 0.7940 (p) cc_final: 0.7674 (p) REVERT: C 91 ARG cc_start: 0.7108 (tpt90) cc_final: 0.6851 (tpt90) REVERT: D 33 TRP cc_start: 0.7864 (p-90) cc_final: 0.7605 (p-90) REVERT: D 87 TRP cc_start: 0.8622 (t60) cc_final: 0.8351 (t60) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.2738 time to fit residues: 171.0427 Evaluate side-chains 390 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 117 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 272 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1349 HIS A1507 HIS ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1644 GLN D 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.119265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.089712 restraints weight = 46085.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093026 restraints weight = 29501.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.093963 restraints weight = 18052.157| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18353 Z= 0.161 Angle : 0.530 9.508 25225 Z= 0.270 Chirality : 0.037 0.177 3151 Planarity : 0.004 0.051 3295 Dihedral : 3.797 19.113 2930 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.17), residues: 2642 helix: 2.71 (0.12), residues: 1822 sheet: -1.60 (0.48), residues: 98 loop : -1.46 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 87 HIS 0.010 0.001 HIS B1599 PHE 0.018 0.001 PHE A1593 TYR 0.013 0.001 TYR A1501 ARG 0.004 0.000 ARG B1424 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 1457) hydrogen bonds : angle 4.14481 ( 4338) metal coordination : bond 0.01182 ( 38) metal coordination : angle 3.55591 ( 30) covalent geometry : bond 0.00311 (18314) covalent geometry : angle 0.51573 (25195) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 TYR cc_start: 0.7999 (m-80) cc_final: 0.7364 (m-80) REVERT: A 543 MET cc_start: 0.8373 (tpt) cc_final: 0.8094 (tpt) REVERT: A 1128 GLN cc_start: 0.8181 (mm110) cc_final: 0.7897 (tp40) REVERT: A 1350 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 1474 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7554 (tm-30) REVERT: A 1492 TRP cc_start: 0.8204 (p-90) cc_final: 0.7870 (p-90) REVERT: A 1582 MET cc_start: 0.7601 (mtt) cc_final: 0.7363 (mtt) REVERT: A 1627 ASN cc_start: 0.8269 (m110) cc_final: 0.7912 (m110) REVERT: A 1653 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 1879 ILE cc_start: 0.7671 (mm) cc_final: 0.7314 (mt) REVERT: B 1313 ARG cc_start: 0.8107 (tpp-160) cc_final: 0.7596 (tpt-90) REVERT: B 1332 ASP cc_start: 0.8653 (t0) cc_final: 0.8420 (t70) REVERT: B 1392 SER cc_start: 0.8198 (p) cc_final: 0.7921 (p) REVERT: B 1421 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7013 (mtm-85) REVERT: B 1475 CYS cc_start: 0.8099 (t) cc_final: 0.7855 (t) REVERT: B 1492 TRP cc_start: 0.8600 (p-90) cc_final: 0.7831 (p-90) REVERT: B 1510 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: B 1582 MET cc_start: 0.7843 (mtp) cc_final: 0.7605 (mtp) REVERT: B 1704 CYS cc_start: 0.8308 (m) cc_final: 0.8106 (m) REVERT: B 1711 CYS cc_start: 0.8001 (m) cc_final: 0.7274 (p) REVERT: B 1728 LEU cc_start: 0.8765 (mp) cc_final: 0.8509 (mp) REVERT: B 1759 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7182 (ptm160) REVERT: B 1779 LEU cc_start: 0.7951 (mt) cc_final: 0.7727 (mm) REVERT: B 1850 PRO cc_start: 0.8512 (Cg_exo) cc_final: 0.8294 (Cg_endo) REVERT: B 1874 CYS cc_start: 0.7846 (p) cc_final: 0.7559 (p) REVERT: C 91 ARG cc_start: 0.7068 (tpt90) cc_final: 0.6830 (tpt90) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.2755 time to fit residues: 171.8742 Evaluate side-chains 388 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 193 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 279 optimal weight: 20.0000 chunk 161 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A1349 HIS A1507 HIS ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2380 GLN B1644 GLN B1932 HIS D 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.085866 restraints weight = 45654.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.088265 restraints weight = 27954.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089908 restraints weight = 19628.436| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18353 Z= 0.230 Angle : 0.575 9.390 25225 Z= 0.303 Chirality : 0.039 0.166 3151 Planarity : 0.005 0.051 3295 Dihedral : 3.959 19.062 2930 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.10 % Allowed : 1.91 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.17), residues: 2642 helix: 2.52 (0.12), residues: 1822 sheet: -1.70 (0.48), residues: 98 loop : -1.52 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 87 HIS 0.008 0.001 HIS B1599 PHE 0.023 0.002 PHE A1593 TYR 0.016 0.001 TYR B1111 ARG 0.007 0.001 ARG B1321 Details of bonding type rmsd hydrogen bonds : bond 0.05747 ( 1457) hydrogen bonds : angle 4.36678 ( 4338) metal coordination : bond 0.01426 ( 38) metal coordination : angle 3.67351 ( 30) covalent geometry : bond 0.00439 (18314) covalent geometry : angle 0.56119 (25195) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: A 76 CYS cc_start: 0.7805 (p) cc_final: 0.7594 (p) REVERT: A 224 TYR cc_start: 0.7032 (t80) cc_final: 0.6724 (t80) REVERT: A 476 TYR cc_start: 0.8094 (m-80) cc_final: 0.7396 (m-80) REVERT: A 543 MET cc_start: 0.8373 (tpt) cc_final: 0.8095 (tpt) REVERT: A 1128 GLN cc_start: 0.7971 (mm110) cc_final: 0.7670 (tp40) REVERT: A 1350 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 1474 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7588 (tm-30) REVERT: A 1492 TRP cc_start: 0.8292 (p-90) cc_final: 0.7868 (p-90) REVERT: A 1582 MET cc_start: 0.7739 (mtt) cc_final: 0.7450 (mtt) REVERT: A 1627 ASN cc_start: 0.8317 (m110) cc_final: 0.7949 (m110) REVERT: A 1652 LEU cc_start: 0.8291 (mt) cc_final: 0.8055 (mm) REVERT: A 1653 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 1779 LEU cc_start: 0.8496 (tp) cc_final: 0.8123 (tt) REVERT: A 1879 ILE cc_start: 0.7723 (mm) cc_final: 0.7364 (mt) REVERT: B 1114 LEU cc_start: 0.8768 (mt) cc_final: 0.8563 (mm) REVERT: B 1332 ASP cc_start: 0.8669 (t0) cc_final: 0.8393 (t70) REVERT: B 1348 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7721 (ttm-80) REVERT: B 1372 TRP cc_start: 0.8180 (t-100) cc_final: 0.7835 (t-100) REVERT: B 1379 LEU cc_start: 0.8583 (tp) cc_final: 0.8376 (tt) REVERT: B 1392 SER cc_start: 0.8145 (p) cc_final: 0.7885 (p) REVERT: B 1421 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7604 (mtm-85) REVERT: B 1475 CYS cc_start: 0.8173 (t) cc_final: 0.7922 (t) REVERT: B 1510 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: B 1582 MET cc_start: 0.7891 (mtp) cc_final: 0.7642 (mtp) REVERT: B 1711 CYS cc_start: 0.8080 (m) cc_final: 0.7381 (p) REVERT: B 1759 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7264 (ptm160) REVERT: B 1779 LEU cc_start: 0.7915 (mt) cc_final: 0.7666 (mm) REVERT: B 1874 CYS cc_start: 0.7892 (p) cc_final: 0.7614 (p) REVERT: C 91 ARG cc_start: 0.7071 (tpt90) cc_final: 0.6852 (tpt90) REVERT: D 33 TRP cc_start: 0.7968 (p-90) cc_final: 0.7732 (p-90) outliers start: 1 outliers final: 1 residues processed: 398 average time/residue: 0.2728 time to fit residues: 167.2190 Evaluate side-chains 380 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 228 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 164 optimal weight: 0.0870 chunk 273 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1507 HIS ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 HIS B1644 GLN D 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088298 restraints weight = 45216.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090730 restraints weight = 27612.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092384 restraints weight = 19315.132| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18353 Z= 0.128 Angle : 0.519 12.913 25225 Z= 0.258 Chirality : 0.037 0.174 3151 Planarity : 0.004 0.047 3295 Dihedral : 3.611 16.987 2930 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.17), residues: 2642 helix: 2.92 (0.12), residues: 1826 sheet: -1.35 (0.49), residues: 95 loop : -1.45 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 87 HIS 0.009 0.001 HIS B1137 PHE 0.022 0.001 PHE A2293 TYR 0.013 0.001 TYR A1501 ARG 0.009 0.000 ARG B1424 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 1457) hydrogen bonds : angle 3.91954 ( 4338) metal coordination : bond 0.00880 ( 38) metal coordination : angle 3.02766 ( 30) covalent geometry : bond 0.00248 (18314) covalent geometry : angle 0.50899 (25195) Misc. bond : bond 0.00457 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.742 Fit side-chains revert: symmetry clash REVERT: A 42 TRP cc_start: 0.7520 (m100) cc_final: 0.7057 (m100) REVERT: A 224 TYR cc_start: 0.6911 (t80) cc_final: 0.6624 (t80) REVERT: A 476 TYR cc_start: 0.8079 (m-80) cc_final: 0.7423 (m-80) REVERT: A 543 MET cc_start: 0.8322 (tpt) cc_final: 0.8050 (tpt) REVERT: A 1128 GLN cc_start: 0.7923 (mm110) cc_final: 0.7639 (tp40) REVERT: A 1350 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7202 (mm-30) REVERT: A 1474 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7553 (tm-30) REVERT: A 1492 TRP cc_start: 0.8286 (p-90) cc_final: 0.7848 (p-90) REVERT: A 1562 ILE cc_start: 0.7882 (tp) cc_final: 0.7682 (tp) REVERT: A 1582 MET cc_start: 0.7630 (mtt) cc_final: 0.7398 (mtt) REVERT: A 1627 ASN cc_start: 0.8208 (m110) cc_final: 0.7776 (m110) REVERT: A 1653 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7246 (tm-30) REVERT: A 1779 LEU cc_start: 0.8482 (tp) cc_final: 0.8091 (tt) REVERT: A 1879 ILE cc_start: 0.7687 (mm) cc_final: 0.7354 (mt) REVERT: A 2414 ARG cc_start: 0.7519 (mmt90) cc_final: 0.7172 (mmm-85) REVERT: B 1313 ARG cc_start: 0.8321 (tpp80) cc_final: 0.7878 (tpp-160) REVERT: B 1332 ASP cc_start: 0.8669 (t0) cc_final: 0.8426 (t70) REVERT: B 1348 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7690 (ttm-80) REVERT: B 1372 TRP cc_start: 0.8152 (t-100) cc_final: 0.7834 (t-100) REVERT: B 1392 SER cc_start: 0.8151 (p) cc_final: 0.7884 (p) REVERT: B 1421 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7468 (mtm-85) REVERT: B 1475 CYS cc_start: 0.8100 (t) cc_final: 0.7846 (t) REVERT: B 1486 ARG cc_start: 0.7680 (mtt90) cc_final: 0.7468 (ttm-80) REVERT: B 1510 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7727 (ttm-80) REVERT: B 1582 MET cc_start: 0.7875 (mtp) cc_final: 0.7383 (mtp) REVERT: B 1704 CYS cc_start: 0.8387 (m) cc_final: 0.8082 (m) REVERT: B 1711 CYS cc_start: 0.8070 (m) cc_final: 0.7423 (p) REVERT: B 1728 LEU cc_start: 0.8755 (mp) cc_final: 0.8432 (mp) REVERT: B 1759 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7162 (ptm160) REVERT: B 1779 LEU cc_start: 0.7927 (mt) cc_final: 0.7674 (mm) REVERT: B 1874 CYS cc_start: 0.7835 (p) cc_final: 0.7556 (p) REVERT: D 33 TRP cc_start: 0.7938 (p-90) cc_final: 0.7732 (p-90) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2669 time to fit residues: 163.8500 Evaluate side-chains 384 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 21 optimal weight: 0.2980 chunk 175 optimal weight: 6.9990 chunk 57 optimal weight: 0.0980 chunk 11 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 47 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A1137 HIS A1349 HIS A1507 HIS ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1644 GLN B1932 HIS D 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.090920 restraints weight = 46011.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.093440 restraints weight = 27692.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.095179 restraints weight = 19121.440| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18353 Z= 0.110 Angle : 0.502 8.637 25225 Z= 0.247 Chirality : 0.036 0.152 3151 Planarity : 0.004 0.045 3295 Dihedral : 3.435 20.270 2930 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.17), residues: 2642 helix: 3.13 (0.12), residues: 1828 sheet: -1.22 (0.51), residues: 90 loop : -1.39 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 87 HIS 0.008 0.001 HIS A1507 PHE 0.020 0.001 PHE A1659 TYR 0.010 0.001 TYR A1501 ARG 0.007 0.000 ARG B1424 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 1457) hydrogen bonds : angle 3.69473 ( 4338) metal coordination : bond 0.00750 ( 38) metal coordination : angle 2.74563 ( 30) covalent geometry : bond 0.00213 (18314) covalent geometry : angle 0.49361 (25195) Misc. bond : bond 0.00826 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: A 224 TYR cc_start: 0.6955 (t80) cc_final: 0.6686 (t80) REVERT: A 476 TYR cc_start: 0.8084 (m-80) cc_final: 0.7399 (m-80) REVERT: A 1128 GLN cc_start: 0.7932 (mm110) cc_final: 0.7647 (tp40) REVERT: A 1348 ARG cc_start: 0.8461 (mtp85) cc_final: 0.7926 (tpp80) REVERT: A 1350 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7290 (mm-30) REVERT: A 1474 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7560 (tm-30) REVERT: A 1492 TRP cc_start: 0.8248 (p-90) cc_final: 0.7803 (p-90) REVERT: A 1582 MET cc_start: 0.7649 (mtt) cc_final: 0.7434 (mtt) REVERT: A 1627 ASN cc_start: 0.8141 (m110) cc_final: 0.7686 (m110) REVERT: A 1653 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7324 (tm-30) REVERT: A 1779 LEU cc_start: 0.8439 (tp) cc_final: 0.8041 (tt) REVERT: A 2414 ARG cc_start: 0.7542 (mmt90) cc_final: 0.7187 (mmm-85) REVERT: B 65 MET cc_start: 0.7035 (tpp) cc_final: 0.6678 (tpp) REVERT: B 1313 ARG cc_start: 0.8253 (tpp80) cc_final: 0.7906 (tpp80) REVERT: B 1332 ASP cc_start: 0.8691 (t0) cc_final: 0.8456 (t0) REVERT: B 1348 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7622 (ttm-80) REVERT: B 1421 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7463 (mtm-85) REVERT: B 1475 CYS cc_start: 0.8067 (t) cc_final: 0.7822 (t) REVERT: B 1510 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7697 (ttm-80) REVERT: B 1582 MET cc_start: 0.7900 (mtp) cc_final: 0.7292 (mtp) REVERT: B 1704 CYS cc_start: 0.8384 (m) cc_final: 0.8088 (m) REVERT: B 1711 CYS cc_start: 0.8095 (m) cc_final: 0.7459 (p) REVERT: B 1728 LEU cc_start: 0.8747 (mp) cc_final: 0.8465 (mp) REVERT: B 1759 ARG cc_start: 0.7761 (ttp-170) cc_final: 0.7192 (ptm160) REVERT: B 1779 LEU cc_start: 0.7918 (mt) cc_final: 0.7667 (mm) REVERT: B 1874 CYS cc_start: 0.7815 (p) cc_final: 0.7526 (p) outliers start: 1 outliers final: 1 residues processed: 400 average time/residue: 0.2612 time to fit residues: 161.5904 Evaluate side-chains 376 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1137 HIS A1349 HIS A1507 HIS ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1644 GLN D 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.087494 restraints weight = 45304.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089934 restraints weight = 27771.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.091576 restraints weight = 19437.034| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18353 Z= 0.180 Angle : 0.534 8.453 25225 Z= 0.274 Chirality : 0.038 0.160 3151 Planarity : 0.004 0.047 3295 Dihedral : 3.564 16.904 2930 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.17), residues: 2642 helix: 2.99 (0.12), residues: 1829 sheet: -1.37 (0.48), residues: 98 loop : -1.35 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 33 HIS 0.007 0.001 HIS A1507 PHE 0.035 0.001 PHE B1659 TYR 0.014 0.001 TYR A1501 ARG 0.007 0.001 ARG B1424 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 1457) hydrogen bonds : angle 3.94814 ( 4338) metal coordination : bond 0.00970 ( 38) metal coordination : angle 3.18157 ( 30) covalent geometry : bond 0.00344 (18314) covalent geometry : angle 0.52317 (25195) Misc. bond : bond 0.00130 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.911 Fit side-chains revert: symmetry clash REVERT: A 224 TYR cc_start: 0.7011 (t80) cc_final: 0.6752 (t80) REVERT: A 476 TYR cc_start: 0.8108 (m-80) cc_final: 0.7437 (m-80) REVERT: A 543 MET cc_start: 0.8344 (tpt) cc_final: 0.8067 (tpt) REVERT: A 1128 GLN cc_start: 0.7942 (mm110) cc_final: 0.7640 (tp40) REVERT: A 1350 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 1474 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7593 (tm-30) REVERT: A 1492 TRP cc_start: 0.8361 (p-90) cc_final: 0.7846 (p-90) REVERT: A 1562 ILE cc_start: 0.7879 (tp) cc_final: 0.7676 (tp) REVERT: A 1582 MET cc_start: 0.7700 (mtt) cc_final: 0.7472 (mtt) REVERT: A 1627 ASN cc_start: 0.8242 (m110) cc_final: 0.7771 (m110) REVERT: A 1653 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 1779 LEU cc_start: 0.8470 (tp) cc_final: 0.8075 (tt) REVERT: A 2414 ARG cc_start: 0.7555 (mmt90) cc_final: 0.7190 (mmm-85) REVERT: B 65 MET cc_start: 0.7013 (tpp) cc_final: 0.6716 (tpp) REVERT: B 1313 ARG cc_start: 0.8272 (tpp80) cc_final: 0.7800 (tpp80) REVERT: B 1332 ASP cc_start: 0.8703 (t0) cc_final: 0.8439 (t70) REVERT: B 1421 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7498 (mtm-85) REVERT: B 1475 CYS cc_start: 0.8130 (t) cc_final: 0.7895 (t) REVERT: B 1510 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7694 (ttm-80) REVERT: B 1582 MET cc_start: 0.7750 (mtp) cc_final: 0.7337 (mtp) REVERT: B 1704 CYS cc_start: 0.8440 (m) cc_final: 0.8140 (m) REVERT: B 1711 CYS cc_start: 0.8078 (m) cc_final: 0.7427 (p) REVERT: B 1728 LEU cc_start: 0.8768 (mp) cc_final: 0.8486 (mp) REVERT: B 1759 ARG cc_start: 0.7814 (ttp-170) cc_final: 0.7213 (ptm160) REVERT: B 1779 LEU cc_start: 0.7918 (mt) cc_final: 0.7673 (mm) REVERT: B 1874 CYS cc_start: 0.7872 (p) cc_final: 0.7577 (p) REVERT: C 99 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6556 (mtm-85) REVERT: D 33 TRP cc_start: 0.7978 (p-90) cc_final: 0.7726 (p-90) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2782 time to fit residues: 170.1078 Evaluate side-chains 369 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 255 optimal weight: 0.0040 chunk 220 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 187 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A1137 HIS A1349 HIS A1507 HIS ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1644 GLN D 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088419 restraints weight = 45123.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090837 restraints weight = 27559.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.092420 restraints weight = 19314.380| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18353 Z= 0.129 Angle : 0.517 9.792 25225 Z= 0.255 Chirality : 0.037 0.156 3151 Planarity : 0.004 0.046 3295 Dihedral : 3.448 17.474 2930 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.17), residues: 2642 helix: 3.11 (0.12), residues: 1831 sheet: -1.19 (0.50), residues: 95 loop : -1.29 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1847 HIS 0.008 0.001 HIS A1507 PHE 0.019 0.001 PHE A1593 TYR 0.020 0.001 TYR B1401 ARG 0.007 0.000 ARG B1348 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 1457) hydrogen bonds : angle 3.77899 ( 4338) metal coordination : bond 0.00753 ( 38) metal coordination : angle 3.13642 ( 30) covalent geometry : bond 0.00253 (18314) covalent geometry : angle 0.50551 (25195) Misc. bond : bond 0.00062 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 TRP cc_start: 0.7297 (m100) cc_final: 0.6935 (m100) REVERT: A 224 TYR cc_start: 0.6954 (t80) cc_final: 0.6690 (t80) REVERT: A 476 TYR cc_start: 0.8077 (m-80) cc_final: 0.7458 (m-80) REVERT: A 1128 GLN cc_start: 0.7905 (mm110) cc_final: 0.7622 (tp40) REVERT: A 1312 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7735 (mtt90) REVERT: A 1348 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7917 (tpp80) REVERT: A 1350 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7234 (mm-30) REVERT: A 1474 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7583 (tm-30) REVERT: A 1492 TRP cc_start: 0.8320 (p-90) cc_final: 0.7838 (p-90) REVERT: A 1562 ILE cc_start: 0.7826 (tp) cc_final: 0.7597 (tp) REVERT: A 1582 MET cc_start: 0.7648 (mtt) cc_final: 0.7433 (mtt) REVERT: A 1627 ASN cc_start: 0.8182 (m110) cc_final: 0.7725 (m110) REVERT: A 1652 LEU cc_start: 0.8237 (mt) cc_final: 0.7980 (mm) REVERT: A 1653 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 1779 LEU cc_start: 0.8461 (tp) cc_final: 0.8074 (tt) REVERT: A 1808 LEU cc_start: 0.9161 (mm) cc_final: 0.8842 (mm) REVERT: A 1879 ILE cc_start: 0.7640 (mm) cc_final: 0.7291 (mt) REVERT: A 2414 ARG cc_start: 0.7555 (mmt90) cc_final: 0.7183 (mmm-85) REVERT: B 65 MET cc_start: 0.7007 (tpp) cc_final: 0.6626 (tpp) REVERT: B 1313 ARG cc_start: 0.8218 (tpp80) cc_final: 0.7726 (tpp80) REVERT: B 1332 ASP cc_start: 0.8689 (t0) cc_final: 0.8441 (t70) REVERT: B 1392 SER cc_start: 0.8176 (p) cc_final: 0.7909 (p) REVERT: B 1421 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7467 (mtm-85) REVERT: B 1475 CYS cc_start: 0.8091 (t) cc_final: 0.7842 (t) REVERT: B 1510 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7704 (ttm-80) REVERT: B 1582 MET cc_start: 0.7735 (mtp) cc_final: 0.7315 (mtp) REVERT: B 1704 CYS cc_start: 0.8443 (m) cc_final: 0.8168 (m) REVERT: B 1711 CYS cc_start: 0.8101 (m) cc_final: 0.7458 (p) REVERT: B 1728 LEU cc_start: 0.8765 (mp) cc_final: 0.8490 (mp) REVERT: B 1759 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7228 (ptm160) REVERT: B 1874 CYS cc_start: 0.7846 (p) cc_final: 0.7548 (p) REVERT: B 1927 LEU cc_start: 0.8571 (mm) cc_final: 0.8344 (mt) REVERT: C 99 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6990 (mtm-85) REVERT: D 33 TRP cc_start: 0.7989 (p-90) cc_final: 0.7754 (p-90) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.2774 time to fit residues: 170.2136 Evaluate side-chains 376 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 54 optimal weight: 0.7980 chunk 249 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 205 optimal weight: 0.0670 chunk 248 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 222 optimal weight: 0.3980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1137 HIS A1349 HIS ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1644 GLN D 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088591 restraints weight = 45226.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090966 restraints weight = 27598.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.092578 restraints weight = 19412.672| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18353 Z= 0.127 Angle : 0.505 8.902 25225 Z= 0.250 Chirality : 0.037 0.157 3151 Planarity : 0.004 0.044 3295 Dihedral : 3.378 16.694 2930 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.17), residues: 2642 helix: 3.16 (0.12), residues: 1834 sheet: -1.07 (0.52), residues: 90 loop : -1.24 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 42 HIS 0.007 0.001 HIS B1770 PHE 0.021 0.001 PHE B1659 TYR 0.016 0.001 TYR B1401 ARG 0.006 0.000 ARG B1424 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1457) hydrogen bonds : angle 3.70514 ( 4338) metal coordination : bond 0.00759 ( 38) metal coordination : angle 3.09688 ( 30) covalent geometry : bond 0.00248 (18314) covalent geometry : angle 0.49436 (25195) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6666.69 seconds wall clock time: 116 minutes 16.00 seconds (6976.00 seconds total)