Starting phenix.real_space_refine on Sun Aug 24 08:08:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7h_18216/08_2025/8q7h_18216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7h_18216/08_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_18216/08_2025/8q7h_18216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7h_18216/08_2025/8q7h_18216.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7h_18216/08_2025/8q7h_18216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7h_18216/08_2025/8q7h_18216.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 61, 'GLN:plan1': 59, 'TYR:plan': 11, 'GLU:plan': 95, 'HIS:plan': 23, 'ASP:plan': 46, 'ASN:plan1': 25, 'PHE:plan': 16, 'TRP:plan': 5} 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: {'ARG:plan': 61, 'GLN:plan1': 60, 'TYR:plan': 14, 'GLU:plan': 84, 'HIS:plan': 21, 'ASP:plan': 39, 'ASN:plan1': 25, 'PHE:plan': 23, 'TRP:plan': 2} 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: {'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 1, 'TYR:plan': 1} 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: {'GLU:plan': 9, 'ASP:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} 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: {'ARG:plan': 5, 'GLU:plan': 6, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLN:plan1': 3} 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: 4.70, per 1000 atoms: 0.26 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: 1.91 Conformation dependent library (CDL) restraints added in 907.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.81 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: 4.32 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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 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: 11.780 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.840 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- 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 : 6.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (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 ARG 0.011 0.001 ARG B1424 TYR 0.019 0.001 TYR B1501 PHE 0.022 0.001 PHE B1650 TRP 0.021 0.001 TRP C 33 HIS 0.007 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00388 (18314) covalent geometry : angle 0.59535 (25195) hydrogen bonds : bond 0.11168 ( 1457) hydrogen bonds : angle 5.49183 ( 4338) metal coordination : bond 0.06666 ( 38) metal coordination : angle 3.30153 ( 30) 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 : 0.450 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: 0.1331 time to fit residues: 86.8436 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 : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A1507 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.120022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089687 restraints weight = 45680.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092003 restraints weight = 28380.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093584 restraints weight = 20099.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094652 restraints weight = 15719.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095415 restraints weight = 13202.589| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18353 Z= 0.127 Angle : 0.513 7.897 25225 Z= 0.262 Chirality : 0.036 0.153 3151 Planarity : 0.004 0.051 3295 Dihedral : 3.824 19.800 2930 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.17), residues: 2642 helix: 2.47 (0.12), residues: 1821 sheet: -1.69 (0.51), residues: 93 loop : -1.57 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1421 TYR 0.012 0.001 TYR B1501 PHE 0.023 0.001 PHE A1522 TRP 0.024 0.001 TRP D 33 HIS 0.011 0.001 HIS B1137 Details of bonding type rmsd covalent geometry : bond 0.00227 (18314) covalent geometry : angle 0.50350 (25195) hydrogen bonds : bond 0.04737 ( 1457) hydrogen bonds : angle 4.18541 ( 4338) metal coordination : bond 0.01289 ( 38) metal coordination : angle 2.82629 ( 30) Misc. bond : bond 0.00508 ( 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 418 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 MET cc_start: 0.8286 (tpt) cc_final: 0.8020 (tpt) REVERT: A 1348 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7831 (tpp80) REVERT: A 1350 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 1365 GLN cc_start: 0.8000 (mp10) cc_final: 0.7404 (mp10) REVERT: A 1492 TRP cc_start: 0.7984 (p-90) cc_final: 0.7773 (p-90) REVERT: A 1515 LEU cc_start: 0.7875 (mt) cc_final: 0.7670 (mt) REVERT: A 1562 ILE cc_start: 0.7946 (tp) cc_final: 0.7704 (tp) REVERT: A 1653 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 1876 LEU cc_start: 0.8849 (mt) cc_final: 0.8509 (mt) REVERT: A 1879 ILE cc_start: 0.7639 (mm) cc_final: 0.7346 (mt) REVERT: B 1318 TYR cc_start: 0.7928 (m-10) cc_final: 0.7555 (m-10) REVERT: B 1332 ASP cc_start: 0.8693 (t0) cc_final: 0.8482 (t0) REVERT: B 1372 TRP cc_start: 0.8078 (t-100) cc_final: 0.7726 (t-100) REVERT: B 1392 SER cc_start: 0.8234 (p) cc_final: 0.7988 (p) REVERT: B 1421 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.6922 (mtm-85) REVERT: B 1422 VAL cc_start: 0.8189 (t) cc_final: 0.7668 (t) REVERT: B 1472 ILE cc_start: 0.8197 (mt) cc_final: 0.7977 (mm) REVERT: B 1475 CYS cc_start: 0.8128 (t) cc_final: 0.7908 (t) REVERT: B 1492 TRP cc_start: 0.8529 (p-90) cc_final: 0.7910 (p-90) REVERT: B 1510 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7750 (ttm-80) REVERT: B 1704 CYS cc_start: 0.8261 (m) cc_final: 0.8052 (m) REVERT: B 1728 LEU cc_start: 0.8762 (mp) cc_final: 0.8472 (mp) REVERT: B 1759 ARG cc_start: 0.7886 (ttp-170) cc_final: 0.7237 (ptm160) REVERT: B 1850 PRO cc_start: 0.8507 (Cg_exo) cc_final: 0.8274 (Cg_endo) REVERT: B 1874 CYS cc_start: 0.7720 (p) cc_final: 0.7506 (p) REVERT: B 1893 LEU cc_start: 0.8930 (tp) cc_final: 0.8660 (tp) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.1329 time to fit residues: 85.4719 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 : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.4988 > 50: distance: 20 - 37: 30.375 distance: 32 - 37: 28.038 distance: 37 - 38: 30.273 distance: 38 - 39: 38.314 distance: 38 - 41: 36.134 distance: 39 - 40: 53.274 distance: 39 - 43: 24.439 distance: 40 - 65: 49.247 distance: 41 - 42: 12.435 distance: 43 - 44: 47.374 distance: 43 - 49: 39.952 distance: 44 - 45: 12.673 distance: 44 - 47: 31.994 distance: 45 - 46: 27.973 distance: 45 - 50: 48.888 distance: 46 - 70: 35.992 distance: 47 - 48: 26.765 distance: 48 - 49: 26.479 distance: 50 - 51: 53.424 distance: 51 - 52: 18.754 distance: 51 - 54: 53.746 distance: 52 - 53: 17.865 distance: 52 - 58: 49.571 distance: 53 - 75: 56.123 distance: 54 - 55: 46.189 distance: 55 - 56: 57.732 distance: 55 - 57: 52.572 distance: 58 - 59: 34.259 distance: 59 - 60: 34.273 distance: 59 - 62: 43.612 distance: 60 - 61: 46.672 distance: 60 - 65: 22.717 distance: 61 - 83: 40.847 distance: 62 - 63: 33.117 distance: 62 - 64: 37.194 distance: 65 - 66: 43.859 distance: 66 - 67: 19.349 distance: 66 - 69: 51.625 distance: 67 - 68: 42.493 distance: 67 - 70: 47.210 distance: 70 - 71: 41.525 distance: 71 - 72: 33.080 distance: 71 - 74: 44.311 distance: 72 - 73: 19.010 distance: 72 - 75: 41.218 distance: 75 - 76: 17.328 distance: 76 - 77: 18.591 distance: 76 - 79: 11.506 distance: 77 - 78: 16.298 distance: 77 - 83: 35.871 distance: 79 - 80: 54.927 distance: 79 - 81: 40.207 distance: 80 - 82: 30.519 distance: 83 - 84: 15.029 distance: 84 - 85: 14.527 distance: 84 - 87: 33.623 distance: 85 - 86: 50.829 distance: 85 - 90: 38.342 distance: 87 - 88: 68.499 distance: 87 - 89: 57.544 distance: 90 - 91: 30.666 distance: 91 - 92: 53.963 distance: 91 - 94: 41.472 distance: 92 - 93: 21.057 distance: 92 - 96: 60.583 distance: 94 - 95: 44.802 distance: 96 - 97: 59.649 distance: 96 - 102: 33.655 distance: 97 - 98: 49.494 distance: 97 - 100: 20.581 distance: 98 - 99: 25.826 distance: 98 - 103: 30.674 distance: 100 - 101: 31.367 distance: 101 - 102: 41.125 distance: 134 - 143: 3.013