Starting phenix.real_space_refine on Thu Feb 15 14:01:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drx_30829/02_2024/7drx_30829_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drx_30829/02_2024/7drx_30829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drx_30829/02_2024/7drx_30829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drx_30829/02_2024/7drx_30829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drx_30829/02_2024/7drx_30829_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drx_30829/02_2024/7drx_30829_updated.pdb" } resolution = 2.9 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= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 60 5.16 5 Be 1 3.05 5 C 8018 2.51 5 N 2046 2.21 5 O 2302 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 168": "NH1" <-> "NH2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 916": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "A ARG 1167": "NH1" <-> "NH2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A TYR 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1257": "NH1" <-> "NH2" Residue "A ARG 1268": "NH1" <-> "NH2" Residue "A TYR 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A TYR 1314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1371": "NH1" <-> "NH2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "A ARG 1434": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12433 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9351 Classifications: {'peptide': 1172} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1133} Chain breaks: 1 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 109 Unusual residues: {' MG': 1, '6PL': 2, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.28, per 1000 atoms: 0.59 Number of scatterers: 12433 At special positions: 0 Unit cell: (150.865, 109.72, 135.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 60 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2302 8.00 N 2046 7.00 C 8018 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 240 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.2 seconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 10 sheets defined 35.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.549A pdb=" N LEU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 272 removed outlier: 3.589A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 removed outlier: 3.523A pdb=" N ALA A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 463' Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 530 through 533 No H-bonds generated for 'chain 'A' and resid 530 through 533' Processing helix chain 'A' and resid 544 through 576 removed outlier: 4.165A pdb=" N ASN A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.764A pdb=" N ALA A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 617 through 633 removed outlier: 3.800A pdb=" N GLU A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 709 through 722 removed outlier: 3.574A pdb=" N ALA A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 775 Processing helix chain 'A' and resid 799 through 811 Processing helix chain 'A' and resid 874 through 877 No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 893 through 906 removed outlier: 3.672A pdb=" N GLU A 906 " --> pdb=" O GLN A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 930 removed outlier: 3.507A pdb=" N LYS A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 935 No H-bonds generated for 'chain 'A' and resid 932 through 935' Processing helix chain 'A' and resid 943 through 951 removed outlier: 3.781A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 980 Processing helix chain 'A' and resid 993 through 1002 Processing helix chain 'A' and resid 1036 through 1047 removed outlier: 3.729A pdb=" N ASN A1046 " --> pdb=" O LYS A1042 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1059 No H-bonds generated for 'chain 'A' and resid 1057 through 1059' Processing helix chain 'A' and resid 1084 through 1095 Processing helix chain 'A' and resid 1107 through 1120 Processing helix chain 'A' and resid 1135 through 1140 Processing helix chain 'A' and resid 1154 through 1157 No H-bonds generated for 'chain 'A' and resid 1154 through 1157' Processing helix chain 'A' and resid 1166 through 1173 removed outlier: 3.602A pdb=" N ALA A1170 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1172 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A1173 " --> pdb=" O ALA A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1199 removed outlier: 3.574A pdb=" N LEU A1184 " --> pdb=" O SER A1180 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 4.432A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1204 No H-bonds generated for 'chain 'A' and resid 1201 through 1204' Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1231 through 1240 removed outlier: 3.583A pdb=" N LEU A1240 " --> pdb=" O PHE A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1251 No H-bonds generated for 'chain 'A' and resid 1248 through 1251' Processing helix chain 'A' and resid 1253 through 1260 removed outlier: 3.921A pdb=" N VAL A1258 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1292 removed outlier: 3.642A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) Proline residue: A1288 - end of helix removed outlier: 3.662A pdb=" N VAL A1291 " --> pdb=" O PHE A1287 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A1292 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1329 removed outlier: 3.517A pdb=" N LEU A1328 " --> pdb=" O ASN A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1346 Processing helix chain 'A' and resid 1348 through 1358 removed outlier: 3.782A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1362 No H-bonds generated for 'chain 'A' and resid 1360 through 1362' Processing helix chain 'A' and resid 1368 through 1372 Processing helix chain 'A' and resid 1376 through 1403 removed outlier: 4.290A pdb=" N PHE A1383 " --> pdb=" O TRP A1379 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Proline residue: A1392 - end of helix removed outlier: 3.509A pdb=" N TYR A1396 " --> pdb=" O PRO A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1416 Processing helix chain 'B' and resid 72 through 97 removed outlier: 3.549A pdb=" N LEU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Proline residue: B 77 - end of helix removed outlier: 3.536A pdb=" N LEU B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.556A pdb=" N TRP B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 387 through 394 Processing sheet with id= A, first strand: chain 'A' and resid 169 through 172 Processing sheet with id= B, first strand: chain 'A' and resid 277 through 280 Processing sheet with id= C, first strand: chain 'A' and resid 406 through 410 removed outlier: 6.923A pdb=" N ASP A 418 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 663 through 666 removed outlier: 6.255A pdb=" N LYS A 984 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SER A 666 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TRP A 986 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A1100 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A1099 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A1011 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A1071 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A1013 " --> pdb=" O VAL A1071 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 687 through 689 removed outlier: 6.862A pdb=" N ALA A 962 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS A 682 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY A 960 " --> pdb=" O CYS A 682 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE A 684 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU A 958 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 913 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 960 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 911 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 962 " --> pdb=" O ARG A 909 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG A 909 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 866 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 838 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 781 through 784 removed outlier: 3.649A pdb=" N GLU A 783 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 830 through 835 removed outlier: 3.721A pdb=" N ILE A 830 " --> pdb=" O MET A 827 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 817 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU A 826 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1145 through 1147 removed outlier: 6.496A pdb=" N TYR A1161 " --> pdb=" O GLY A1146 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.203A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 141 through 145 383 hydrogen bonds defined for protein. 1095 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: 4.39 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2041 1.32 - 1.44: 3468 1.44 - 1.56: 7112 1.56 - 1.68: 5 1.68 - 1.81: 92 Bond restraints: 12718 Sorted by residual: bond pdb=" BE BEF A1602 " pdb=" F1 BEF A1602 " ideal model delta sigma weight residual 1.476 1.762 -0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" BE BEF A1602 " pdb=" F3 BEF A1602 " ideal model delta sigma weight residual 1.476 1.760 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" BE BEF A1602 " pdb=" F2 BEF A1602 " ideal model delta sigma weight residual 1.476 1.760 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" N GLU A1409 " pdb=" CA GLU A1409 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.28e-02 6.10e+03 8.25e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.57e+00 ... (remaining 12713 not shown) Histogram of bond angle deviations from ideal: 97.21 - 105.79: 239 105.79 - 114.38: 7376 114.38 - 122.96: 8723 122.96 - 131.55: 855 131.55 - 140.13: 36 Bond angle restraints: 17229 Sorted by residual: angle pdb=" C PHE A1063 " pdb=" N PRO A1064 " pdb=" CA PRO A1064 " ideal model delta sigma weight residual 127.00 140.13 -13.13 2.40e+00 1.74e-01 2.99e+01 angle pdb=" C PHE A1063 " pdb=" N PRO A1064 " pdb=" CD PRO A1064 " ideal model delta sigma weight residual 120.60 109.81 10.79 2.20e+00 2.07e-01 2.40e+01 angle pdb=" N LYS A 276 " pdb=" CA LYS A 276 " pdb=" C LYS A 276 " ideal model delta sigma weight residual 110.91 116.60 -5.69 1.17e+00 7.31e-01 2.37e+01 angle pdb=" N ILE B 403 " pdb=" CA ILE B 403 " pdb=" C ILE B 403 " ideal model delta sigma weight residual 111.91 107.80 4.11 8.90e-01 1.26e+00 2.14e+01 angle pdb=" CA TRP A 398 " pdb=" CB TRP A 398 " pdb=" CG TRP A 398 " ideal model delta sigma weight residual 113.60 121.89 -8.29 1.90e+00 2.77e-01 1.91e+01 ... (remaining 17224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.95: 7333 19.95 - 39.91: 236 39.91 - 59.86: 33 59.86 - 79.81: 7 79.81 - 99.76: 5 Dihedral angle restraints: 7614 sinusoidal: 3138 harmonic: 4476 Sorted by residual: dihedral pdb=" CA PHE B 398 " pdb=" C PHE B 398 " pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta harmonic sigma weight residual 180.00 148.79 31.21 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA GLN A1331 " pdb=" C GLN A1331 " pdb=" N TYR A1332 " pdb=" CA TYR A1332 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA PHE A1365 " pdb=" C PHE A1365 " pdb=" N PHE A1366 " pdb=" CA PHE A1366 " ideal model delta harmonic sigma weight residual 180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 7611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1669 0.090 - 0.180: 216 0.180 - 0.269: 17 0.269 - 0.359: 0 0.359 - 0.449: 1 Chirality restraints: 1903 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.06e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 240 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.85 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1900 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.031 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" C PHE B 398 " -0.104 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.039 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.030 2.00e-02 2.50e+03 5.84e-02 3.41e+01 pdb=" C VAL A1408 " -0.101 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.037 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.038 2.00e-02 2.50e+03 3.47e-02 3.00e+01 pdb=" CG TRP B 142 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " -0.000 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 285 2.69 - 3.24: 11622 3.24 - 3.79: 19574 3.79 - 4.35: 27635 4.35 - 4.90: 43911 Nonbonded interactions: 103027 Sorted by model distance: nonbonded pdb=" OD1 ASP A 667 " pdb="MG MG A1601 " model vdw 2.134 2.170 nonbonded pdb=" OD2 ASP A 667 " pdb=" F1 BEF A1602 " model vdw 2.213 2.390 nonbonded pdb=" OD2 ASP A 667 " pdb="MG MG A1601 " model vdw 2.241 2.170 nonbonded pdb=" O THR A 669 " pdb=" F1 BEF A1602 " model vdw 2.247 2.390 nonbonded pdb=" O CYS B 216 " pdb=" OG SER B 220 " model vdw 2.270 2.440 ... (remaining 103022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 1.710 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: 7.200 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.280 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:16.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.008 0.286 12718 Z= 0.559 Angle : 0.956 13.129 17229 Z= 0.520 Chirality : 0.060 0.449 1903 Planarity : 0.007 0.072 2179 Dihedral : 11.055 99.762 4738 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.07 % Allowed : 2.10 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.72 (0.16), residues: 1528 helix: -4.11 (0.10), residues: 596 sheet: -1.68 (0.34), residues: 198 loop : -2.60 (0.19), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.005 TRP B 142 HIS 0.007 0.002 HIS B 186 PHE 0.047 0.004 PHE A1287 TYR 0.040 0.003 TYR A 618 ARG 0.010 0.001 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7342 (ttm) cc_final: 0.7125 (ttp) REVERT: A 464 ARG cc_start: 0.7758 (mtm180) cc_final: 0.6329 (ppt170) REVERT: A 1010 MET cc_start: 0.8498 (mtt) cc_final: 0.8235 (mtt) REVERT: A 1222 MET cc_start: 0.8042 (mtp) cc_final: 0.7740 (mtm) REVERT: A 1234 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8277 (p) REVERT: B 315 MET cc_start: 0.9067 (mmm) cc_final: 0.8809 (mmm) REVERT: B 403 ILE cc_start: 0.6593 (mm) cc_final: 0.6389 (mm) outliers start: 1 outliers final: 2 residues processed: 262 average time/residue: 1.3338 time to fit residues: 379.5173 Evaluate side-chains 154 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 1234 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 411 ASN A 477 ASN A 497 ASN A 504 ASN A 534 ASN A 685 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 HIS A 797 GLN A1061 HIS A1096 ASN A1176 HIS A1245 ASN A1307 HIS A1330 HIS ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 171 ASN B 255 ASN B 256 ASN B 341 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12718 Z= 0.248 Angle : 0.658 9.192 17229 Z= 0.346 Chirality : 0.046 0.185 1903 Planarity : 0.005 0.051 2179 Dihedral : 9.716 87.401 1837 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.70 % Allowed : 8.40 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -3.07 (0.19), residues: 1528 helix: -2.04 (0.17), residues: 603 sheet: -1.27 (0.34), residues: 205 loop : -2.19 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 142 HIS 0.004 0.001 HIS A1176 PHE 0.025 0.002 PHE A1365 TYR 0.021 0.002 TYR B 280 ARG 0.009 0.000 ARG A 731 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.6171 (mp0) cc_final: 0.5458 (mt-10) REVERT: A 402 LYS cc_start: 0.7966 (mttt) cc_final: 0.7689 (mtmt) REVERT: A 457 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7465 (mmt90) REVERT: A 464 ARG cc_start: 0.7833 (mtm180) cc_final: 0.5937 (tmm160) REVERT: A 898 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7983 (tp) REVERT: A 1011 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: A 1036 LEU cc_start: 0.7429 (mp) cc_final: 0.7078 (mm) REVERT: A 1222 MET cc_start: 0.8169 (mtp) cc_final: 0.7950 (mtm) outliers start: 36 outliers final: 15 residues processed: 184 average time/residue: 1.3060 time to fit residues: 261.8975 Evaluate side-chains 158 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 196 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 0.0470 chunk 94 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 0.0570 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 111 optimal weight: 0.0170 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 497 ASN A 571 ASN A 660 GLN A 685 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN B 60 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12718 Z= 0.155 Angle : 0.563 8.384 17229 Z= 0.294 Chirality : 0.043 0.198 1903 Planarity : 0.003 0.046 2179 Dihedral : 8.259 86.386 1834 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.62 % Allowed : 9.90 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1528 helix: -0.70 (0.20), residues: 594 sheet: -1.25 (0.33), residues: 215 loop : -1.92 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 142 HIS 0.002 0.001 HIS A 475 PHE 0.024 0.001 PHE A1365 TYR 0.023 0.001 TYR B 280 ARG 0.004 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7445 (mmt90) REVERT: A 464 ARG cc_start: 0.7807 (mtm180) cc_final: 0.6232 (tmt170) REVERT: A 1011 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: A 1036 LEU cc_start: 0.7213 (mp) cc_final: 0.6943 (mm) REVERT: A 1402 PHE cc_start: 0.7970 (m-10) cc_final: 0.7769 (m-10) REVERT: B 127 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: B 170 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7737 (mtpp) REVERT: B 403 ILE cc_start: 0.6686 (mm) cc_final: 0.6445 (mm) outliers start: 35 outliers final: 14 residues processed: 181 average time/residue: 1.2266 time to fit residues: 242.4980 Evaluate side-chains 154 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 170 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 93 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12718 Z= 0.272 Angle : 0.614 8.200 17229 Z= 0.318 Chirality : 0.045 0.171 1903 Planarity : 0.004 0.045 2179 Dihedral : 8.170 86.010 1834 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.52 % Allowed : 10.42 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.65 (0.21), residues: 1528 helix: -0.28 (0.21), residues: 598 sheet: -1.14 (0.33), residues: 218 loop : -1.76 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 398 HIS 0.004 0.001 HIS A1330 PHE 0.024 0.002 PHE A1365 TYR 0.023 0.002 TYR B 280 ARG 0.005 0.000 ARG A1087 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 146 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: A 202 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 457 ARG cc_start: 0.7855 (mmm160) cc_final: 0.7488 (mmt90) REVERT: A 464 ARG cc_start: 0.7822 (mtm180) cc_final: 0.6253 (ppt170) REVERT: A 523 MET cc_start: 0.7596 (tpp) cc_final: 0.7283 (tpp) REVERT: A 1077 LEU cc_start: 0.8262 (tp) cc_final: 0.8050 (tt) REVERT: A 1222 MET cc_start: 0.8245 (mtp) cc_final: 0.7953 (mtm) REVERT: B 127 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: B 269 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7419 (t0) REVERT: B 333 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: B 390 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7277 (tt) REVERT: B 403 ILE cc_start: 0.6641 (mm) cc_final: 0.6313 (mm) outliers start: 47 outliers final: 27 residues processed: 173 average time/residue: 1.2022 time to fit residues: 229.7664 Evaluate side-chains 169 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.0770 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12718 Z= 0.220 Angle : 0.586 8.128 17229 Z= 0.303 Chirality : 0.044 0.169 1903 Planarity : 0.003 0.045 2179 Dihedral : 7.881 87.197 1834 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.22 % Allowed : 11.39 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.21), residues: 1528 helix: 0.02 (0.21), residues: 603 sheet: -0.97 (0.34), residues: 216 loop : -1.69 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 398 HIS 0.004 0.001 HIS A1330 PHE 0.023 0.002 PHE A1365 TYR 0.022 0.002 TYR B 280 ARG 0.004 0.000 ARG A1087 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 202 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7870 (p) REVERT: A 464 ARG cc_start: 0.7813 (mtm180) cc_final: 0.6208 (tmt170) REVERT: A 523 MET cc_start: 0.7624 (tpp) cc_final: 0.7318 (tpp) REVERT: A 731 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6834 (ptp-170) REVERT: A 765 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6716 (mmp-170) REVERT: A 1036 LEU cc_start: 0.7398 (mp) cc_final: 0.6977 (mm) REVERT: A 1222 MET cc_start: 0.8229 (mtp) cc_final: 0.8000 (mtm) REVERT: B 127 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: B 169 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: B 269 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7441 (t0) REVERT: B 333 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: B 390 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7291 (tt) outliers start: 43 outliers final: 20 residues processed: 168 average time/residue: 1.2326 time to fit residues: 227.3572 Evaluate side-chains 161 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 731 ARG Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 550 ASN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12718 Z= 0.331 Angle : 0.659 8.395 17229 Z= 0.340 Chirality : 0.047 0.181 1903 Planarity : 0.004 0.044 2179 Dihedral : 8.119 89.216 1832 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.60 % Allowed : 11.17 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.21), residues: 1528 helix: -0.00 (0.21), residues: 601 sheet: -0.90 (0.34), residues: 217 loop : -1.66 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 398 HIS 0.006 0.001 HIS A1330 PHE 0.025 0.002 PHE A1365 TYR 0.024 0.002 TYR B 280 ARG 0.008 0.001 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7307 (mtt) REVERT: A 202 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7905 (p) REVERT: A 276 LYS cc_start: 0.7754 (mmtt) cc_final: 0.6992 (mmtm) REVERT: A 457 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7522 (mmt90) REVERT: A 464 ARG cc_start: 0.7820 (mtm180) cc_final: 0.5916 (tmm160) REVERT: A 523 MET cc_start: 0.7590 (tpp) cc_final: 0.7276 (tpp) REVERT: A 731 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6765 (ptp-170) REVERT: A 765 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6714 (mmp-170) REVERT: A 1036 LEU cc_start: 0.7621 (mp) cc_final: 0.7191 (mm) REVERT: A 1062 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6793 (mp0) REVERT: A 1222 MET cc_start: 0.8264 (mtp) cc_final: 0.8055 (mtm) REVERT: B 169 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7967 (mtt) REVERT: B 333 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: B 356 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8750 (mttm) REVERT: B 390 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7369 (tt) outliers start: 48 outliers final: 29 residues processed: 170 average time/residue: 1.1699 time to fit residues: 218.5772 Evaluate side-chains 177 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 731 ARG Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 82 optimal weight: 0.0770 chunk 147 optimal weight: 0.0870 chunk 92 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12718 Z= 0.161 Angle : 0.558 7.870 17229 Z= 0.289 Chirality : 0.043 0.181 1903 Planarity : 0.003 0.044 2179 Dihedral : 7.568 88.849 1832 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.62 % Allowed : 12.97 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.11 (0.21), residues: 1528 helix: 0.29 (0.22), residues: 602 sheet: -0.74 (0.35), residues: 207 loop : -1.61 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 348 HIS 0.001 0.000 HIS A1330 PHE 0.019 0.001 PHE A1365 TYR 0.023 0.001 TYR B 280 ARG 0.009 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 4.089 Fit side-chains revert: symmetry clash REVERT: A 202 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7716 (t) REVERT: A 276 LYS cc_start: 0.7622 (mmtt) cc_final: 0.6880 (mmtm) REVERT: A 464 ARG cc_start: 0.7787 (mtm180) cc_final: 0.6277 (ppt170) REVERT: A 523 MET cc_start: 0.7676 (tpp) cc_final: 0.7371 (tpp) REVERT: A 1036 LEU cc_start: 0.7320 (mp) cc_final: 0.6962 (mm) REVERT: A 1222 MET cc_start: 0.8229 (mtp) cc_final: 0.7976 (mtm) REVERT: B 127 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: B 170 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7657 (mtpp) outliers start: 35 outliers final: 18 residues processed: 169 average time/residue: 1.2757 time to fit residues: 236.8646 Evaluate side-chains 161 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 115 optimal weight: 0.0870 chunk 134 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12718 Z= 0.212 Angle : 0.585 7.861 17229 Z= 0.302 Chirality : 0.044 0.176 1903 Planarity : 0.003 0.047 2179 Dihedral : 7.622 87.348 1832 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.00 % Allowed : 12.97 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.05 (0.21), residues: 1528 helix: 0.33 (0.22), residues: 602 sheet: -0.73 (0.35), residues: 214 loop : -1.56 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 398 HIS 0.003 0.001 HIS A1330 PHE 0.022 0.001 PHE A1365 TYR 0.023 0.001 TYR B 280 ARG 0.008 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 202 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7765 (t) REVERT: A 276 LYS cc_start: 0.7671 (mmtt) cc_final: 0.6919 (mmtm) REVERT: A 464 ARG cc_start: 0.7786 (mtm180) cc_final: 0.6171 (tmt170) REVERT: A 523 MET cc_start: 0.7665 (tpp) cc_final: 0.7379 (tpp) REVERT: A 1036 LEU cc_start: 0.7414 (mp) cc_final: 0.7068 (mm) REVERT: A 1222 MET cc_start: 0.8253 (mtp) cc_final: 0.8007 (mtm) REVERT: B 127 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: B 170 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7682 (mtpp) REVERT: B 333 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: B 356 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8705 (mttm) REVERT: B 390 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7301 (tt) outliers start: 40 outliers final: 25 residues processed: 161 average time/residue: 1.1522 time to fit residues: 204.0265 Evaluate side-chains 172 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 GLN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12718 Z= 0.210 Angle : 0.583 7.904 17229 Z= 0.301 Chirality : 0.044 0.172 1903 Planarity : 0.003 0.048 2179 Dihedral : 7.614 84.435 1832 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.00 % Allowed : 13.19 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.00 (0.21), residues: 1528 helix: 0.35 (0.21), residues: 605 sheet: -0.59 (0.35), residues: 206 loop : -1.56 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 348 HIS 0.003 0.001 HIS A1330 PHE 0.021 0.001 PHE A1365 TYR 0.023 0.001 TYR B 280 ARG 0.008 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 145 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 202 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7751 (t) REVERT: A 276 LYS cc_start: 0.7695 (mmtt) cc_final: 0.6935 (mmtm) REVERT: A 464 ARG cc_start: 0.7783 (mtm180) cc_final: 0.6167 (tmt170) REVERT: A 523 MET cc_start: 0.7612 (tpp) cc_final: 0.7273 (tpp) REVERT: A 765 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6707 (mmp-170) REVERT: A 876 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7690 (pt) REVERT: A 1036 LEU cc_start: 0.7425 (mp) cc_final: 0.7085 (mm) REVERT: A 1222 MET cc_start: 0.8253 (mtp) cc_final: 0.8005 (mtm) REVERT: B 127 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: B 170 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7670 (mtpp) REVERT: B 333 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7408 (m-30) REVERT: B 356 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8687 (mttm) REVERT: B 390 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7307 (tt) outliers start: 40 outliers final: 25 residues processed: 163 average time/residue: 1.1798 time to fit residues: 211.1129 Evaluate side-chains 176 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12718 Z= 0.227 Angle : 0.595 7.879 17229 Z= 0.308 Chirality : 0.044 0.182 1903 Planarity : 0.003 0.047 2179 Dihedral : 7.675 81.599 1832 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.85 % Allowed : 13.57 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.96 (0.21), residues: 1528 helix: 0.37 (0.21), residues: 605 sheet: -0.62 (0.34), residues: 214 loop : -1.52 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 348 HIS 0.004 0.001 HIS A1330 PHE 0.022 0.001 PHE A1365 TYR 0.024 0.002 TYR B 280 ARG 0.008 0.000 ARG A 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.558 Fit side-chains REVERT: A 202 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7773 (t) REVERT: A 276 LYS cc_start: 0.7720 (mmtt) cc_final: 0.6957 (mmtm) REVERT: A 464 ARG cc_start: 0.7784 (mtm180) cc_final: 0.5869 (tmm160) REVERT: A 523 MET cc_start: 0.7613 (tpp) cc_final: 0.7314 (tpp) REVERT: A 765 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6685 (mmp-170) REVERT: A 876 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7716 (pt) REVERT: A 1036 LEU cc_start: 0.7489 (mp) cc_final: 0.7132 (mm) REVERT: A 1222 MET cc_start: 0.8243 (mtp) cc_final: 0.7997 (mtm) REVERT: B 127 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: B 170 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7676 (mtpp) REVERT: B 333 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: B 356 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8677 (mttm) REVERT: B 390 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7322 (tt) outliers start: 38 outliers final: 26 residues processed: 165 average time/residue: 1.2113 time to fit residues: 220.1187 Evaluate side-chains 179 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 437 ASN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113071 restraints weight = 15291.140| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.55 r_work: 0.3148 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12718 Z= 0.304 Angle : 0.656 8.437 17229 Z= 0.339 Chirality : 0.047 0.195 1903 Planarity : 0.004 0.048 2179 Dihedral : 8.079 72.756 1832 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.85 % Allowed : 13.72 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.08 (0.21), residues: 1528 helix: 0.21 (0.21), residues: 614 sheet: -0.58 (0.34), residues: 213 loop : -1.58 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 398 HIS 0.005 0.001 HIS A1330 PHE 0.024 0.002 PHE A1365 TYR 0.024 0.002 TYR B 280 ARG 0.009 0.001 ARG A 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4718.28 seconds wall clock time: 84 minutes 45.65 seconds (5085.65 seconds total)