Starting phenix.real_space_refine on Fri Aug 9 09:25:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p82_17539/08_2024/8p82_17539.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p82_17539/08_2024/8p82_17539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p82_17539/08_2024/8p82_17539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p82_17539/08_2024/8p82_17539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p82_17539/08_2024/8p82_17539.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p82_17539/08_2024/8p82_17539.cif" } resolution = 3.36 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= 0.012 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 6 6.06 5 S 192 5.16 5 C 15902 2.51 5 N 4380 2.21 5 O 4676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1821": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25156 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1596, 12575 Classifications: {'peptide': 1596} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 90, 'TRANS': 1503} Chain breaks: 11 Chain: "B" Number of atoms: 12575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1596, 12575 Classifications: {'peptide': 1596} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 90, 'TRANS': 1503} Chain breaks: 11 Chain: "A" 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: "B" 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 4242 SG CYS A1179 102.662 174.460 42.172 1.00 82.06 S ATOM 4467 SG CYS A1208 100.265 171.693 42.995 1.00 97.65 S ATOM 4489 SG CYS A1211 98.982 175.056 42.891 1.00102.52 S ATOM 4652 SG CYS A1232 99.906 173.669 39.843 1.00103.23 S ATOM 4489 SG CYS A1211 98.982 175.056 42.891 1.00102.52 S ATOM 4518 SG CYS A1215 97.375 178.287 44.941 1.00104.99 S ATOM 4666 SG CYS A1234 97.265 177.751 41.100 1.00 98.99 S ATOM 4719 SG CYS A1240 100.257 178.830 42.642 1.00105.25 S ATOM 4382 SG CYS A1196 89.088 175.575 40.445 1.00129.79 S ATOM 4406 SG CYS A1199 89.113 178.903 39.781 1.00148.65 S ATOM 16817 SG CYS B1179 56.081 71.440 42.173 1.00 82.06 S ATOM 17042 SG CYS B1208 58.467 74.212 43.006 1.00 97.65 S ATOM 17064 SG CYS B1211 59.761 70.854 42.895 1.00102.52 S ATOM 17227 SG CYS B1232 58.836 72.246 39.849 1.00103.23 S ATOM 17064 SG CYS B1211 59.761 70.854 42.895 1.00102.52 S ATOM 17093 SG CYS B1215 61.376 67.622 44.938 1.00104.99 S ATOM 17241 SG CYS B1234 61.489 68.169 41.098 1.00 98.99 S ATOM 17294 SG CYS B1240 58.498 67.077 42.634 1.00105.25 S ATOM 16957 SG CYS B1196 69.659 70.372 40.459 1.00129.79 S ATOM 16981 SG CYS B1199 69.646 67.046 39.786 1.00148.65 S Time building chain proxies: 13.52, per 1000 atoms: 0.54 Number of scatterers: 25156 At special positions: 0 Unit cell: (158.756, 248.196, 103.974, 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 6 29.99 S 192 16.00 O 4676 8.00 N 4380 7.00 C 15902 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.88 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1211 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1232 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1208 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1179 " pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1234 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1240 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1215 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1211 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" ND1 HIS A1216 " pdb="ZN ZN A3002 " - pdb=" ND1 HIS A1219 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1199 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1196 " pdb=" ZN B3000 " pdb="ZN ZN B3000 " - pdb=" SG CYS B1211 " pdb="ZN ZN B3000 " - pdb=" SG CYS B1232 " pdb="ZN ZN B3000 " - pdb=" SG CYS B1208 " pdb="ZN ZN B3000 " - pdb=" SG CYS B1179 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1234 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1240 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1215 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1211 " pdb=" ZN B3002 " pdb="ZN ZN B3002 " - pdb=" ND1 HIS B1216 " pdb="ZN ZN B3002 " - pdb=" ND1 HIS B1219 " pdb="ZN ZN B3002 " - pdb=" SG CYS B1199 " pdb="ZN ZN B3002 " - pdb=" SG CYS B1196 " Number of angles added : 28 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6076 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 26 sheets defined 53.0% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 14 through 32 removed outlier: 3.788A pdb=" N LYS A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 removed outlier: 4.846A pdb=" N VAL A 42 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 787 through 793 removed outlier: 3.620A pdb=" N PHE A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 874 through 883 Processing helix chain 'A' and resid 884 through 901 Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 916 through 920 removed outlier: 3.646A pdb=" N ARG A 920 " --> pdb=" O ASP A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'A' and resid 934 through 941 removed outlier: 3.792A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1095 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1108 Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1125 through 1143 Processing helix chain 'A' and resid 1144 through 1146 No H-bonds generated for 'chain 'A' and resid 1144 through 1146' Processing helix chain 'A' and resid 1149 through 1159 removed outlier: 3.754A pdb=" N VAL A1153 " --> pdb=" O LYS A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1167 Processing helix chain 'A' and resid 1168 through 1176 removed outlier: 3.587A pdb=" N CYS A1174 " --> pdb=" O LEU A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1185 Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'A' and resid 1209 through 1215 Processing helix chain 'A' and resid 1233 through 1238 Processing helix chain 'A' and resid 1247 through 1262 Processing helix chain 'A' and resid 1263 through 1267 Processing helix chain 'A' and resid 1274 through 1291 removed outlier: 3.811A pdb=" N VAL A1288 " --> pdb=" O ALA A1284 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS A1291 " --> pdb=" O THR A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1333 Processing helix chain 'A' and resid 1335 through 1344 Processing helix chain 'A' and resid 1364 through 1372 removed outlier: 3.595A pdb=" N GLN A1368 " --> pdb=" O LEU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1390 removed outlier: 3.512A pdb=" N ILE A1388 " --> pdb=" O THR A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1410 Processing helix chain 'A' and resid 1416 through 1443 removed outlier: 3.738A pdb=" N SER A1431 " --> pdb=" O ARG A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1467 Processing helix chain 'A' and resid 1467 through 1488 removed outlier: 3.771A pdb=" N GLU A1473 " --> pdb=" O PRO A1469 " (cutoff:3.500A) Proline residue: A1485 - end of helix Processing helix chain 'A' and resid 1502 through 1515 removed outlier: 4.026A pdb=" N GLY A1509 " --> pdb=" O ASP A1505 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A1510 " --> pdb=" O ALA A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1716 removed outlier: 4.457A pdb=" N TRP A1716 " --> pdb=" O ARG A1712 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1802 removed outlier: 3.821A pdb=" N SER A1780 " --> pdb=" O SER A1776 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A1790 " --> pdb=" O ARG A1786 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A1791 " --> pdb=" O ALA A1787 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1802 " --> pdb=" O LEU A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1809 Processing helix chain 'A' and resid 1820 through 1863 removed outlier: 3.525A pdb=" N LEU A1835 " --> pdb=" O VAL A1831 " (cutoff:3.500A) Proline residue: A1837 - end of helix Processing helix chain 'A' and resid 1909 through 1928 removed outlier: 3.544A pdb=" N HIS A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1943 No H-bonds generated for 'chain 'A' and resid 1941 through 1943' Processing helix chain 'A' and resid 1944 through 1967 Processing helix chain 'A' and resid 2043 through 2048 Processing helix chain 'A' and resid 2048 through 2053 Processing helix chain 'A' and resid 2054 through 2057 removed outlier: 3.798A pdb=" N LEU A2057 " --> pdb=" O PRO A2054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2054 through 2057' Processing helix chain 'A' and resid 2062 through 2067 removed outlier: 3.809A pdb=" N LEU A2066 " --> pdb=" O ARG A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2120 Processing helix chain 'A' and resid 2165 through 2169 Processing helix chain 'A' and resid 2181 through 2189 removed outlier: 3.747A pdb=" N LEU A2185 " --> pdb=" O SER A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2200 Processing helix chain 'A' and resid 2203 through 2207 Processing helix chain 'A' and resid 2210 through 2216 Processing helix chain 'A' and resid 2217 through 2235 removed outlier: 3.540A pdb=" N LYS A2221 " --> pdb=" O GLY A2217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A2227 " --> pdb=" O SER A2223 " (cutoff:3.500A) Processing helix chain 'A' and resid 2247 through 2265 Processing helix chain 'A' and resid 2288 through 2305 Processing helix chain 'A' and resid 2311 through 2317 removed outlier: 3.622A pdb=" N ASN A2317 " --> pdb=" O CYS A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2522 through 2542 Processing helix chain 'A' and resid 2551 through 2559 Processing helix chain 'A' and resid 2564 through 2572 removed outlier: 3.618A pdb=" N ALA A2569 " --> pdb=" O TRP A2565 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A2570 " --> pdb=" O HIS A2566 " (cutoff:3.500A) Processing helix chain 'A' and resid 2572 through 2587 Processing helix chain 'A' and resid 2590 through 2599 removed outlier: 3.634A pdb=" N ASP A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) Processing helix chain 'A' and resid 2607 through 2611 Processing helix chain 'A' and resid 2620 through 2624 Processing helix chain 'A' and resid 2630 through 2644 Processing helix chain 'A' and resid 2647 through 2660 Processing helix chain 'A' and resid 2663 through 2668 Processing helix chain 'A' and resid 2671 through 2680 Processing helix chain 'A' and resid 2686 through 2694 Processing helix chain 'A' and resid 2703 through 2721 Processing helix chain 'A' and resid 2722 through 2735 Processing helix chain 'A' and resid 2779 through 2793 Processing helix chain 'B' and resid 14 through 32 removed outlier: 3.788A pdb=" N LYS B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 44 removed outlier: 4.846A pdb=" N VAL B 42 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 449 through 452 Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 787 through 793 removed outlier: 3.619A pdb=" N PHE B 791 " --> pdb=" O SER B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 874 through 883 Processing helix chain 'B' and resid 884 through 901 Processing helix chain 'B' and resid 904 through 913 Processing helix chain 'B' and resid 916 through 920 removed outlier: 3.645A pdb=" N ARG B 920 " --> pdb=" O ASP B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 930 Processing helix chain 'B' and resid 934 through 941 removed outlier: 3.792A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1095 Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1101 through 1108 Processing helix chain 'B' and resid 1115 through 1123 Processing helix chain 'B' and resid 1125 through 1143 Processing helix chain 'B' and resid 1144 through 1146 No H-bonds generated for 'chain 'B' and resid 1144 through 1146' Processing helix chain 'B' and resid 1149 through 1159 removed outlier: 3.754A pdb=" N VAL B1153 " --> pdb=" O LYS B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1167 Processing helix chain 'B' and resid 1168 through 1176 removed outlier: 3.586A pdb=" N CYS B1174 " --> pdb=" O LEU B1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1185 Processing helix chain 'B' and resid 1198 through 1200 No H-bonds generated for 'chain 'B' and resid 1198 through 1200' Processing helix chain 'B' and resid 1209 through 1215 Processing helix chain 'B' and resid 1233 through 1238 Processing helix chain 'B' and resid 1247 through 1262 Processing helix chain 'B' and resid 1263 through 1267 Processing helix chain 'B' and resid 1274 through 1291 removed outlier: 3.811A pdb=" N VAL B1288 " --> pdb=" O ALA B1284 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS B1291 " --> pdb=" O THR B1287 " (cutoff:3.500A) Processing helix chain 'B' and resid 1323 through 1333 Processing helix chain 'B' and resid 1335 through 1344 Processing helix chain 'B' and resid 1364 through 1372 removed outlier: 3.594A pdb=" N GLN B1368 " --> pdb=" O LEU B1364 " (cutoff:3.500A) Processing helix chain 'B' and resid 1377 through 1390 removed outlier: 3.512A pdb=" N ILE B1388 " --> pdb=" O THR B1384 " (cutoff:3.500A) Processing helix chain 'B' and resid 1395 through 1410 Processing helix chain 'B' and resid 1416 through 1443 removed outlier: 3.739A pdb=" N SER B1431 " --> pdb=" O ARG B1427 " (cutoff:3.500A) Processing helix chain 'B' and resid 1454 through 1467 Processing helix chain 'B' and resid 1467 through 1488 removed outlier: 3.772A pdb=" N GLU B1473 " --> pdb=" O PRO B1469 " (cutoff:3.500A) Proline residue: B1485 - end of helix Processing helix chain 'B' and resid 1502 through 1515 removed outlier: 4.026A pdb=" N GLY B1509 " --> pdb=" O ASP B1505 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B1510 " --> pdb=" O ALA B1506 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1716 removed outlier: 4.457A pdb=" N TRP B1716 " --> pdb=" O ARG B1712 " (cutoff:3.500A) Processing helix chain 'B' and resid 1776 through 1802 removed outlier: 3.821A pdb=" N SER B1780 " --> pdb=" O SER B1776 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B1790 " --> pdb=" O ARG B1786 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B1791 " --> pdb=" O ALA B1787 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B1802 " --> pdb=" O LEU B1798 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1809 Processing helix chain 'B' and resid 1820 through 1863 removed outlier: 3.552A pdb=" N LEU B1835 " --> pdb=" O VAL B1831 " (cutoff:3.500A) Proline residue: B1837 - end of helix Processing helix chain 'B' and resid 1909 through 1928 removed outlier: 3.545A pdb=" N HIS B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) Processing helix chain 'B' and resid 1941 through 1943 No H-bonds generated for 'chain 'B' and resid 1941 through 1943' Processing helix chain 'B' and resid 1944 through 1967 Processing helix chain 'B' and resid 2043 through 2048 Processing helix chain 'B' and resid 2048 through 2053 Processing helix chain 'B' and resid 2054 through 2057 removed outlier: 3.798A pdb=" N LEU B2057 " --> pdb=" O PRO B2054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2054 through 2057' Processing helix chain 'B' and resid 2062 through 2067 removed outlier: 3.809A pdb=" N LEU B2066 " --> pdb=" O ARG B2062 " (cutoff:3.500A) Processing helix chain 'B' and resid 2104 through 2120 Processing helix chain 'B' and resid 2165 through 2169 Processing helix chain 'B' and resid 2181 through 2189 removed outlier: 3.746A pdb=" N LEU B2185 " --> pdb=" O SER B2181 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2200 Processing helix chain 'B' and resid 2203 through 2207 Processing helix chain 'B' and resid 2210 through 2216 Processing helix chain 'B' and resid 2217 through 2235 removed outlier: 3.539A pdb=" N LYS B2221 " --> pdb=" O GLY B2217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B2227 " --> pdb=" O SER B2223 " (cutoff:3.500A) Processing helix chain 'B' and resid 2247 through 2265 Processing helix chain 'B' and resid 2288 through 2305 Processing helix chain 'B' and resid 2311 through 2317 removed outlier: 3.622A pdb=" N ASN B2317 " --> pdb=" O CYS B2314 " (cutoff:3.500A) Processing helix chain 'B' and resid 2522 through 2542 Processing helix chain 'B' and resid 2551 through 2559 Processing helix chain 'B' and resid 2564 through 2572 removed outlier: 3.618A pdb=" N ALA B2569 " --> pdb=" O TRP B2565 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B2570 " --> pdb=" O HIS B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2587 Processing helix chain 'B' and resid 2590 through 2599 removed outlier: 3.634A pdb=" N ASP B2599 " --> pdb=" O PHE B2595 " (cutoff:3.500A) Processing helix chain 'B' and resid 2607 through 2611 Processing helix chain 'B' and resid 2620 through 2624 Processing helix chain 'B' and resid 2630 through 2644 Processing helix chain 'B' and resid 2647 through 2660 Processing helix chain 'B' and resid 2663 through 2668 Processing helix chain 'B' and resid 2671 through 2680 Processing helix chain 'B' and resid 2686 through 2694 Processing helix chain 'B' and resid 2703 through 2721 Processing helix chain 'B' and resid 2722 through 2735 Processing helix chain 'B' and resid 2779 through 2793 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 4.046A pdb=" N SER A 843 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A 872 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE A 841 " --> pdb=" O GLU A 872 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 394 removed outlier: 3.508A pdb=" N CYS A 373 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE A 372 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU A 427 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 374 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 429 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 376 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 433 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THR A 445 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR A 461 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 478 removed outlier: 6.737A pdb=" N LEU A 491 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS A 736 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP A 493 " --> pdb=" O THR A 734 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N THR A 734 " --> pdb=" O TRP A 493 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 745 through 752 removed outlier: 5.761A pdb=" N ILE A 746 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS A 761 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 748 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL A 766 " --> pdb=" O ASN A 783 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASN A 783 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR A 768 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU A 781 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 770 " --> pdb=" O GLU A 779 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 800 through 803 removed outlier: 3.874A pdb=" N ALA A 800 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 813 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1189 through 1190 removed outlier: 4.046A pdb=" N ILE A1189 " --> pdb=" O ALA A1230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1207 through 1208 Processing sheet with id=AB1, first strand: chain 'A' and resid 2240 through 2244 removed outlier: 6.014A pdb=" N LEU A2240 " --> pdb=" O LYS A2278 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THR A2280 " --> pdb=" O LEU A2240 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A2242 " --> pdb=" O THR A2280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 2505 through 2506 Processing sheet with id=AB3, first strand: chain 'A' and resid 2603 through 2605 Processing sheet with id=AB4, first strand: chain 'A' and resid 2695 through 2698 Processing sheet with id=AB5, first strand: chain 'B' and resid 2 through 10 removed outlier: 4.046A pdb=" N SER B 843 " --> pdb=" O ALA B 870 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU B 872 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 841 " --> pdb=" O GLU B 872 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 53 Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 53 Processing sheet with id=AB8, first strand: chain 'B' and resid 390 through 394 removed outlier: 3.509A pdb=" N CYS B 373 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE B 372 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU B 427 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 374 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA B 429 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 376 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 433 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THR B 445 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR B 461 " --> pdb=" O THR B 445 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 473 through 478 removed outlier: 6.737A pdb=" N LEU B 491 " --> pdb=" O LYS B 736 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS B 736 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TRP B 493 " --> pdb=" O THR B 734 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR B 734 " --> pdb=" O TRP B 493 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 745 through 752 removed outlier: 5.762A pdb=" N ILE B 746 " --> pdb=" O LYS B 761 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS B 761 " --> pdb=" O ILE B 746 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA B 748 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL B 766 " --> pdb=" O ASN B 783 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASN B 783 " --> pdb=" O VAL B 766 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR B 768 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU B 781 " --> pdb=" O TYR B 768 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 770 " --> pdb=" O GLU B 779 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 800 through 803 removed outlier: 3.873A pdb=" N ALA B 800 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 813 " --> pdb=" O ALA B 800 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1189 through 1190 removed outlier: 4.046A pdb=" N ILE B1189 " --> pdb=" O ALA B1230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1207 through 1208 Processing sheet with id=AC5, first strand: chain 'B' and resid 2240 through 2244 removed outlier: 6.014A pdb=" N LEU B2240 " --> pdb=" O LYS B2278 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THR B2280 " --> pdb=" O LEU B2240 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU B2242 " --> pdb=" O THR B2280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 2505 through 2506 Processing sheet with id=AC7, first strand: chain 'B' and resid 2603 through 2605 Processing sheet with id=AC8, first strand: chain 'B' and resid 2695 through 2698 1268 hydrogen bonds defined for protein. 3558 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: 11.16 Time building geometry restraints manager: 9.84 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: 8148 1.34 - 1.47: 4026 1.47 - 1.59: 13218 1.59 - 1.71: 0 1.71 - 1.83: 284 Bond restraints: 25676 Sorted by residual: bond pdb=" CA PRO B2547 " pdb=" CB PRO B2547 " ideal model delta sigma weight residual 1.532 1.548 -0.017 7.10e-03 1.98e+04 5.53e+00 bond pdb=" CA PRO A2547 " pdb=" CB PRO A2547 " ideal model delta sigma weight residual 1.532 1.548 -0.017 7.10e-03 1.98e+04 5.46e+00 bond pdb=" N ARG A2511 " pdb=" CA ARG A2511 " ideal model delta sigma weight residual 1.454 1.481 -0.027 1.19e-02 7.06e+03 5.22e+00 bond pdb=" N LEU B2762 " pdb=" CA LEU B2762 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.32e-02 5.74e+03 5.20e+00 bond pdb=" N LEU A2762 " pdb=" CA LEU A2762 " ideal model delta sigma weight residual 1.453 1.483 -0.029 1.32e-02 5.74e+03 4.94e+00 ... (remaining 25671 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.38: 998 106.38 - 113.35: 14140 113.35 - 120.31: 9314 120.31 - 127.27: 10075 127.27 - 134.24: 275 Bond angle restraints: 34802 Sorted by residual: angle pdb=" CA PHE B2675 " pdb=" CB PHE B2675 " pdb=" CG PHE B2675 " ideal model delta sigma weight residual 113.80 119.01 -5.21 1.00e+00 1.00e+00 2.71e+01 angle pdb=" CA PHE A2675 " pdb=" CB PHE A2675 " pdb=" CG PHE A2675 " ideal model delta sigma weight residual 113.80 118.99 -5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" N PHE A2675 " pdb=" CA PHE A2675 " pdb=" CB PHE A2675 " ideal model delta sigma weight residual 110.06 102.98 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" N PHE B2675 " pdb=" CA PHE B2675 " pdb=" CB PHE B2675 " ideal model delta sigma weight residual 110.06 102.98 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" N ARG B2511 " pdb=" CA ARG B2511 " pdb=" C ARG B2511 " ideal model delta sigma weight residual 109.95 117.13 -7.18 1.59e+00 3.96e-01 2.04e+01 ... (remaining 34797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14627 17.90 - 35.79: 870 35.79 - 53.69: 138 53.69 - 71.58: 53 71.58 - 89.48: 22 Dihedral angle restraints: 15710 sinusoidal: 6384 harmonic: 9326 Sorted by residual: dihedral pdb=" CA GLU A 807 " pdb=" C GLU A 807 " pdb=" N SER A 808 " pdb=" CA SER A 808 " ideal model delta harmonic sigma weight residual 180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLU B 807 " pdb=" C GLU B 807 " pdb=" N SER B 808 " pdb=" CA SER B 808 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ARG B 78 " pdb=" C ARG B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 15707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2173 0.069 - 0.138: 1359 0.138 - 0.206: 358 0.206 - 0.275: 28 0.275 - 0.344: 4 Chirality restraints: 3922 Sorted by residual: chirality pdb=" CA THR A 818 " pdb=" N THR A 818 " pdb=" C THR A 818 " pdb=" CB THR A 818 " both_signs ideal model delta sigma weight residual False 2.53 2.87 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA THR B 818 " pdb=" N THR B 818 " pdb=" C THR B 818 " pdb=" CB THR B 818 " both_signs ideal model delta sigma weight residual False 2.53 2.87 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA ARG A 78 " pdb=" N ARG A 78 " pdb=" C ARG A 78 " pdb=" CB ARG A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 3919 not shown) Planarity restraints: 4512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A2576 " -0.068 2.00e-02 2.50e+03 3.58e-02 2.56e+01 pdb=" CG TYR A2576 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A2576 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A2576 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A2576 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A2576 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A2576 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A2576 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B2576 " -0.068 2.00e-02 2.50e+03 3.58e-02 2.56e+01 pdb=" CG TYR B2576 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B2576 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B2576 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B2576 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B2576 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B2576 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B2576 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B2675 " 0.054 2.00e-02 2.50e+03 3.58e-02 2.24e+01 pdb=" CG PHE B2675 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE B2675 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B2675 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B2675 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B2675 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B2675 " 0.021 2.00e-02 2.50e+03 ... (remaining 4509 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2108 2.76 - 3.29: 26463 3.29 - 3.83: 40062 3.83 - 4.36: 51309 4.36 - 4.90: 82140 Nonbonded interactions: 202082 Sorted by model distance: nonbonded pdb=" OG1 THR A1498 " pdb=" CE MET B1910 " model vdw 2.221 3.460 nonbonded pdb=" O ALA B1858 " pdb=" OG SER B1861 " model vdw 2.283 3.040 nonbonded pdb=" O ALA A1858 " pdb=" OG SER A1861 " model vdw 2.284 3.040 nonbonded pdb=" OE1 GLU A1367 " pdb=" OG SER B1861 " model vdw 2.293 3.040 nonbonded pdb=" OG1 THR B 933 " pdb=" OE2 GLU B 937 " model vdw 2.311 3.040 ... (remaining 202077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.81 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.840 Check model and map are aligned: 0.130 Set scattering table: 0.210 Process input model: 71.680 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 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 : 0.013 0.074 25676 Z= 0.858 Angle : 1.108 8.276 34802 Z= 0.659 Chirality : 0.085 0.344 3922 Planarity : 0.011 0.123 4512 Dihedral : 12.801 89.477 9634 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.78 % Favored : 96.02 % Rotamer: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.17 % 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: -0.97 (0.14), residues: 3144 helix: -0.85 (0.11), residues: 1456 sheet: 0.10 (0.30), residues: 294 loop : -0.36 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP B2733 HIS 0.018 0.003 HIS A 477 PHE 0.072 0.006 PHE B2675 TYR 0.068 0.007 TYR B2576 ARG 0.006 0.001 ARG B1257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 827 MET cc_start: 0.8893 (mmm) cc_final: 0.8673 (mmp) REVERT: A 2064 GLU cc_start: 0.7511 (tt0) cc_final: 0.6470 (pp20) REVERT: B 1 MET cc_start: 0.4535 (mtt) cc_final: 0.4295 (ttm) REVERT: B 29 LEU cc_start: 0.8377 (mt) cc_final: 0.7959 (tt) REVERT: B 1451 ASN cc_start: 0.8542 (m-40) cc_final: 0.8189 (p0) REVERT: B 1714 MET cc_start: 0.6586 (mtm) cc_final: 0.5965 (mtp) REVERT: B 2064 GLU cc_start: 0.7911 (tt0) cc_final: 0.6859 (pp20) outliers start: 2 outliers final: 1 residues processed: 296 average time/residue: 0.4110 time to fit residues: 184.4638 Evaluate side-chains 162 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1956 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.0000 chunk 241 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 0.0470 chunk 128 optimal weight: 0.8980 chunk 249 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 288 optimal weight: 4.9990 overall best weight: 0.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 780 GLN A1281 GLN A1290 HIS B 430 ASN B 780 GLN B1176 ASN B1281 GLN B1290 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25676 Z= 0.185 Angle : 0.656 11.232 34802 Z= 0.342 Chirality : 0.042 0.168 3922 Planarity : 0.005 0.079 4512 Dihedral : 5.405 47.456 3426 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.71 % Allowed : 6.13 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.81 (0.15), residues: 3144 helix: 1.10 (0.13), residues: 1458 sheet: -0.09 (0.27), residues: 324 loop : 0.25 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1841 HIS 0.008 0.001 HIS B2262 PHE 0.020 0.002 PHE A2675 TYR 0.016 0.002 TYR B2638 ARG 0.007 0.001 ARG B 797 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 LEU cc_start: 0.8420 (mt) cc_final: 0.7996 (tt) REVERT: B 1451 ASN cc_start: 0.8536 (m-40) cc_final: 0.8228 (p0) REVERT: B 1714 MET cc_start: 0.6783 (mtm) cc_final: 0.6122 (mtt) outliers start: 20 outliers final: 6 residues processed: 200 average time/residue: 0.3936 time to fit residues: 121.9500 Evaluate side-chains 154 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1516 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain B residue 772 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.0770 chunk 89 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 289 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 257 optimal weight: 0.0570 chunk 286 optimal weight: 0.9980 chunk 98 optimal weight: 0.0070 chunk 232 optimal weight: 6.9990 overall best weight: 0.4274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25676 Z= 0.149 Angle : 0.585 11.536 34802 Z= 0.296 Chirality : 0.039 0.150 3922 Planarity : 0.005 0.049 4512 Dihedral : 4.707 26.000 3424 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.71 % Allowed : 6.88 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.35 (0.15), residues: 3144 helix: 1.60 (0.14), residues: 1460 sheet: -0.00 (0.27), residues: 332 loop : 0.51 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1841 HIS 0.005 0.001 HIS B2652 PHE 0.022 0.001 PHE A2303 TYR 0.018 0.001 TYR A2638 ARG 0.008 0.000 ARG A2636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 ASP cc_start: 0.6959 (p0) cc_final: 0.6618 (p0) REVERT: A 827 MET cc_start: 0.8993 (tpp) cc_final: 0.8413 (tmm) REVERT: A 2114 MET cc_start: 0.8528 (tpp) cc_final: 0.8306 (tpp) REVERT: B 29 LEU cc_start: 0.8413 (mt) cc_final: 0.7923 (tt) REVERT: B 881 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8054 (tt) REVERT: B 1451 ASN cc_start: 0.8516 (m-40) cc_final: 0.8179 (p0) REVERT: B 1714 MET cc_start: 0.6775 (mtm) cc_final: 0.6560 (mtm) REVERT: B 1961 MET cc_start: 0.8274 (mmt) cc_final: 0.8039 (mmm) outliers start: 20 outliers final: 7 residues processed: 185 average time/residue: 0.4223 time to fit residues: 121.9521 Evaluate side-chains 151 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1941 VAL Chi-restraints excluded: chain A residue 2023 PHE Chi-restraints excluded: chain A residue 2634 TYR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 1488 MET Chi-restraints excluded: chain B residue 2634 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 194 optimal weight: 0.1980 chunk 290 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 ASN A1508 GLN A1829 ASN B 463 GLN B 795 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25676 Z= 0.256 Angle : 0.634 10.296 34802 Z= 0.321 Chirality : 0.041 0.148 3922 Planarity : 0.005 0.049 4512 Dihedral : 4.690 23.546 3424 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.86 % Allowed : 8.55 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.24 (0.15), residues: 3144 helix: 1.50 (0.14), residues: 1476 sheet: -0.20 (0.27), residues: 330 loop : 0.50 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1841 HIS 0.009 0.002 HIS A 410 PHE 0.020 0.002 PHE A2675 TYR 0.026 0.002 TYR B2638 ARG 0.011 0.001 ARG B2517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 ASP cc_start: 0.5812 (OUTLIER) cc_final: 0.4678 (p0) REVERT: A 827 MET cc_start: 0.8926 (tpp) cc_final: 0.8425 (tmm) REVERT: B 772 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.4310 (p0) REVERT: B 881 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 1451 ASN cc_start: 0.8404 (m-40) cc_final: 0.8118 (p0) REVERT: B 1714 MET cc_start: 0.7088 (mtm) cc_final: 0.6371 (mtt) outliers start: 24 outliers final: 11 residues processed: 161 average time/residue: 0.3561 time to fit residues: 93.8851 Evaluate side-chains 142 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 1502 THR Chi-restraints excluded: chain A residue 1516 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 2634 TYR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1502 THR Chi-restraints excluded: chain B residue 2599 ASP Chi-restraints excluded: chain B residue 2634 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 262 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 275 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25676 Z= 0.185 Angle : 0.575 8.178 34802 Z= 0.289 Chirality : 0.039 0.139 3922 Planarity : 0.005 0.046 4512 Dihedral : 4.495 22.456 3424 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.21 % Allowed : 8.84 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.37 (0.15), residues: 3144 helix: 1.67 (0.14), residues: 1470 sheet: -0.20 (0.27), residues: 330 loop : 0.49 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1841 HIS 0.005 0.001 HIS B 9 PHE 0.016 0.001 PHE B2675 TYR 0.013 0.001 TYR A2638 ARG 0.007 0.001 ARG B2636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 ASP cc_start: 0.5781 (OUTLIER) cc_final: 0.4661 (p0) REVERT: A 827 MET cc_start: 0.8955 (tpp) cc_final: 0.8563 (tmm) REVERT: A 1344 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8514 (mmp) REVERT: B 772 ASP cc_start: 0.5699 (OUTLIER) cc_final: 0.4502 (p0) REVERT: B 881 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8352 (tt) REVERT: B 1451 ASN cc_start: 0.8245 (m-40) cc_final: 0.7965 (p0) REVERT: B 1714 MET cc_start: 0.6901 (mtm) cc_final: 0.6244 (mtt) REVERT: B 1961 MET cc_start: 0.8819 (mmm) cc_final: 0.8358 (tpp) outliers start: 34 outliers final: 15 residues processed: 162 average time/residue: 0.3605 time to fit residues: 95.0402 Evaluate side-chains 152 residues out of total 2806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1502 THR Chi-restraints excluded: chain A residue 1516 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1911 MET Chi-restraints excluded: chain A residue 1941 VAL Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2634 TYR Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 1439 LEU Chi-restraints excluded: chain B residue 1488 MET Chi-restraints excluded: chain B residue 1502 THR Chi-restraints excluded: chain B residue 1836 ILE Chi-restraints excluded: chain B residue 2634 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 180 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3993 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: