Starting phenix.real_space_refine on Sat Apr 6 21:57:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmj_17761/04_2024/8pmj_17761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmj_17761/04_2024/8pmj_17761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmj_17761/04_2024/8pmj_17761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmj_17761/04_2024/8pmj_17761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmj_17761/04_2024/8pmj_17761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmj_17761/04_2024/8pmj_17761_updated.pdb" } resolution = 2.81 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 5 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 5774 2.51 5 N 1503 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A GLU 934": "OE1" <-> "OE2" Residue "A GLU 1296": "OE1" <-> "OE2" Residue "A GLU 1302": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8985 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8805 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 32, 'TRANS': 1100} Chain breaks: 4 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 180 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'CLR': 4, 'VO4': 1} Classifications: {'undetermined': 9, 'water': 3} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N VAL A 248 " occ=0.96 ... (5 atoms not shown) pdb=" CG2 VAL A 248 " occ=0.68 Time building chain proxies: 5.36, per 1000 atoms: 0.60 Number of scatterers: 8985 At special positions: 0 Unit cell: (104.94, 100.98, 127.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 52 16.00 P 5 15.00 Mg 2 11.99 O 1648 8.00 N 1503 7.00 C 5774 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: 3.54 Conformation dependent library (CDL) restraints added in 1.7 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 4 sheets defined 64.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.673A pdb=" N PHE A 51 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 99 removed outlier: 4.330A pdb=" N GLN A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Proline residue: A 77 - end of helix removed outlier: 3.637A pdb=" N ASP A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 184 removed outlier: 3.568A pdb=" N ARG A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 195 through 213 removed outlier: 4.772A pdb=" N ILE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 236 removed outlier: 3.696A pdb=" N GLY A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 286 Proline residue: A 250 - end of helix removed outlier: 3.807A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 297 through 343 removed outlier: 3.708A pdb=" N PHE A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 326 " --> pdb=" O MET A 322 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 397 removed outlier: 3.537A pdb=" N VAL A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Proline residue: A 378 - end of helix removed outlier: 4.169A pdb=" N THR A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.723A pdb=" N LEU A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 491 through 496 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 561 through 575 removed outlier: 4.156A pdb=" N ARG A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 603 removed outlier: 3.575A pdb=" N VAL A 600 " --> pdb=" O MET A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 620 No H-bonds generated for 'chain 'A' and resid 617 through 620' Processing helix chain 'A' and resid 740 through 780 removed outlier: 4.175A pdb=" N ALA A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Proline residue: A 750 - end of helix Proline residue: A 753 - end of helix removed outlier: 4.005A pdb=" N THR A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) Proline residue: A 770 - end of helix removed outlier: 3.745A pdb=" N ALA A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 840 removed outlier: 3.624A pdb=" N SER A 809 " --> pdb=" O MET A 805 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 821 " --> pdb=" O GLY A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 854 through 872 removed outlier: 4.419A pdb=" N ALA A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 894 Processing helix chain 'A' and resid 898 through 945 removed outlier: 4.063A pdb=" N VAL A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Proline residue: A 909 - end of helix removed outlier: 3.588A pdb=" N ALA A 912 " --> pdb=" O PHE A 908 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY A 924 " --> pdb=" O ARG A 920 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 925 " --> pdb=" O MET A 921 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 928 " --> pdb=" O GLY A 924 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 953 Processing helix chain 'A' and resid 956 through 1009 removed outlier: 4.511A pdb=" N LYS A 969 " --> pdb=" O THR A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.991A pdb=" N THR A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 975 " --> pdb=" O PHE A 971 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN A 976 " --> pdb=" O LYS A 972 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1027 Processing helix chain 'A' and resid 1030 through 1036 removed outlier: 3.873A pdb=" N ALA A1034 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE A1035 " --> pdb=" O GLY A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1055 removed outlier: 4.270A pdb=" N ALA A1042 " --> pdb=" O PRO A1039 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A1045 " --> pdb=" O ALA A1042 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1054 " --> pdb=" O PHE A1051 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A1055 " --> pdb=" O PHE A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 removed outlier: 3.565A pdb=" N ILE A1123 " --> pdb=" O LYS A1119 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) 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 1155 removed outlier: 3.671A pdb=" N ASN A1155 " --> pdb=" O PHE A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 4.483A pdb=" N GLY A1177 " --> pdb=" O ASN A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1194 Processing helix chain 'A' and resid 1198 through 1202 Processing helix chain 'A' and resid 1214 through 1216 No H-bonds generated for 'chain 'A' and resid 1214 through 1216' Processing helix chain 'A' and resid 1221 through 1235 removed outlier: 4.067A pdb=" N ARG A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1264 removed outlier: 3.649A pdb=" N THR A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A1263 " --> pdb=" O VAL A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1279 No H-bonds generated for 'chain 'A' and resid 1277 through 1279' Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1309 through 1316 Processing sheet with id= A, first strand: chain 'A' and resid 443 through 445 removed outlier: 3.626A pdb=" N MET A 443 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 633 through 636 removed outlier: 6.679A pdb=" N ILE A 610 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 453 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER A 612 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY A 455 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1101 through 1103 removed outlier: 3.549A pdb=" N LYS A1136 " --> pdb=" O VAL A1081 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1293 through 1298 removed outlier: 6.738A pdb=" N VAL A1288 " --> pdb=" O ILE A1295 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A1297 " --> pdb=" O ILE A1286 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A1286 " --> pdb=" O LYS A1297 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS A1270 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A1111 " --> pdb=" O CYS A1270 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A1272 " --> pdb=" O PHE A1111 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY A1113 " --> pdb=" O VAL A1272 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2890 1.35 - 1.49: 2275 1.49 - 1.62: 3909 1.62 - 1.76: 0 1.76 - 1.90: 89 Bond restraints: 9163 Sorted by residual: bond pdb=" C4 ADP A1506 " pdb=" C5 ADP A1506 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C5 ADP A1506 " pdb=" C6 ADP A1506 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O3B ADP A1506 " pdb=" PB ADP A1506 " ideal model delta sigma weight residual 1.510 1.463 0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C8 ADP A1506 " pdb=" N7 ADP A1506 " ideal model delta sigma weight residual 1.350 1.306 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" N LYS A 829 " pdb=" CA LYS A 829 " ideal model delta sigma weight residual 1.458 1.486 -0.027 1.26e-02 6.30e+03 4.72e+00 ... (remaining 9158 not shown) Histogram of bond angle deviations from ideal: 95.70 - 104.54: 135 104.54 - 113.38: 5104 113.38 - 122.22: 5986 122.22 - 131.06: 1164 131.06 - 139.90: 30 Bond angle restraints: 12419 Sorted by residual: angle pdb=" PA ADP A1506 " pdb=" O3A ADP A1506 " pdb=" PB ADP A1506 " ideal model delta sigma weight residual 120.50 136.49 -15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" C TYR A1037 " pdb=" N THR A1038 " pdb=" CA THR A1038 " ideal model delta sigma weight residual 120.09 125.08 -4.99 1.25e+00 6.40e-01 1.60e+01 angle pdb=" CA MET A 86 " pdb=" C MET A 86 " pdb=" O MET A 86 " ideal model delta sigma weight residual 120.55 116.61 3.94 1.06e+00 8.90e-01 1.38e+01 angle pdb=" O ALA A 739 " pdb=" C ALA A 739 " pdb=" N PRO A 740 " ideal model delta sigma weight residual 121.37 118.13 3.24 9.00e-01 1.23e+00 1.29e+01 angle pdb=" C LYS A 829 " pdb=" N ARG A 830 " pdb=" CA ARG A 830 " ideal model delta sigma weight residual 120.28 115.75 4.53 1.34e+00 5.57e-01 1.14e+01 ... (remaining 12414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4967 17.41 - 34.81: 492 34.81 - 52.22: 148 52.22 - 69.63: 31 69.63 - 87.04: 9 Dihedral angle restraints: 5647 sinusoidal: 2401 harmonic: 3246 Sorted by residual: dihedral pdb=" O1B ADP A1506 " pdb=" O3A ADP A1506 " pdb=" PB ADP A1506 " pdb=" PA ADP A1506 " ideal model delta sinusoidal sigma weight residual -60.00 27.03 -87.04 1 2.00e+01 2.50e-03 2.28e+01 dihedral pdb=" CA MET A 138 " pdb=" C MET A 138 " pdb=" N ILE A 139 " pdb=" CA ILE A 139 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CG ARG A1050 " pdb=" CD ARG A1050 " pdb=" NE ARG A1050 " pdb=" CZ ARG A1050 " ideal model delta sinusoidal sigma weight residual 90.00 41.05 48.95 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 5644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 1417 0.177 - 0.354: 1 0.354 - 0.531: 0 0.531 - 0.708: 0 0.708 - 0.886: 1 Chirality restraints: 1419 Sorted by residual: chirality pdb=" V VO4 A1507 " pdb=" O1 VO4 A1507 " pdb=" O2 VO4 A1507 " pdb=" O4 VO4 A1507 " both_signs ideal model delta sigma weight residual True 5.36 4.48 0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C3' ADP A1506 " pdb=" C2' ADP A1506 " pdb=" C4' ADP A1506 " pdb=" O3' ADP A1506 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA MET A 138 " pdb=" N MET A 138 " pdb=" C MET A 138 " pdb=" CB MET A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1416 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 828 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C THR A 828 " 0.036 2.00e-02 2.50e+03 pdb=" O THR A 828 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 829 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 534 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" CD GLU A 534 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 534 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 534 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 776 " 0.011 2.00e-02 2.50e+03 1.24e-02 2.70e+00 pdb=" CG PHE A 776 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 776 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 776 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 776 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 776 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 776 " 0.000 2.00e-02 2.50e+03 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 53 2.55 - 3.13: 7019 3.13 - 3.72: 14051 3.72 - 4.31: 20019 4.31 - 4.90: 33191 Nonbonded interactions: 74333 Sorted by model distance: nonbonded pdb="MG MG A1508 " pdb=" O HOH A1602 " model vdw 1.958 2.170 nonbonded pdb=" O3G ATP A1501 " pdb="MG MG A1509 " model vdw 1.958 2.170 nonbonded pdb="MG MG A1509 " pdb=" O HOH A1601 " model vdw 1.986 2.170 nonbonded pdb=" OG SER A 462 " pdb="MG MG A1509 " model vdw 1.995 2.170 nonbonded pdb=" OE1 GLN A1161 " pdb="MG MG A1508 " model vdw 2.017 2.170 ... (remaining 74328 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=0.00 max=1.00 mean=0.91 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: 4.910 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: 13.500 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.090 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.112 9163 Z= 0.237 Angle : 0.640 15.993 12419 Z= 0.336 Chirality : 0.047 0.886 1419 Planarity : 0.003 0.039 1551 Dihedral : 15.655 87.036 3561 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1123 helix: 1.02 (0.19), residues: 748 sheet: 0.40 (0.60), residues: 76 loop : -1.18 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1071 HIS 0.004 0.001 HIS A 615 PHE 0.029 0.001 PHE A 776 TYR 0.025 0.001 TYR A 337 ARG 0.012 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 594 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8219 (tm-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 1.4824 time to fit residues: 183.6824 Evaluate side-chains 94 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.0370 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 307 ASN A 312 GLN A 530 GLN A 885 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9163 Z= 0.276 Angle : 0.601 8.987 12419 Z= 0.312 Chirality : 0.043 0.157 1419 Planarity : 0.004 0.030 1551 Dihedral : 7.566 65.970 1525 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.53 % Allowed : 13.46 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1123 helix: 1.17 (0.19), residues: 740 sheet: -0.03 (0.55), residues: 74 loop : -1.13 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.004 0.001 HIS A 428 PHE 0.027 0.002 PHE A 776 TYR 0.019 0.002 TYR A 337 ARG 0.009 0.001 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7784 (tp40) REVERT: A 526 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: A 554 GLU cc_start: 0.7688 (tp30) cc_final: 0.7371 (tp30) REVERT: A 779 ILE cc_start: 0.7654 (mm) cc_final: 0.7212 (mt) REVERT: A 1252 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7337 (tp30) outliers start: 33 outliers final: 16 residues processed: 131 average time/residue: 1.4386 time to fit residues: 200.0884 Evaluate side-chains 117 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1252 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.0030 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN A 778 GLN A 885 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9163 Z= 0.148 Angle : 0.487 8.416 12419 Z= 0.254 Chirality : 0.039 0.144 1419 Planarity : 0.003 0.033 1551 Dihedral : 6.720 77.100 1525 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.88 % Allowed : 14.96 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1123 helix: 1.60 (0.19), residues: 741 sheet: 0.07 (0.56), residues: 74 loop : -1.06 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.000 HIS A 615 PHE 0.023 0.001 PHE A 776 TYR 0.018 0.001 TYR A 337 ARG 0.008 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7603 (t0) cc_final: 0.7345 (t0) REVERT: A 243 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4671 (pp) REVERT: A 476 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: A 526 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: A 778 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7119 (mp-120) REVERT: A 957 ARG cc_start: 0.7721 (mpp80) cc_final: 0.7498 (mtt90) REVERT: A 989 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6656 (mm-40) outliers start: 27 outliers final: 15 residues processed: 126 average time/residue: 1.4170 time to fit residues: 189.7072 Evaluate side-chains 120 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 778 GLN Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1279 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 530 GLN A 778 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9163 Z= 0.195 Angle : 0.512 8.187 12419 Z= 0.266 Chirality : 0.040 0.157 1419 Planarity : 0.003 0.031 1551 Dihedral : 6.692 78.086 1525 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.74 % Allowed : 14.64 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1123 helix: 1.60 (0.19), residues: 739 sheet: 0.16 (0.55), residues: 74 loop : -1.09 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 314 HIS 0.002 0.001 HIS A 428 PHE 0.025 0.001 PHE A 776 TYR 0.014 0.001 TYR A 337 ARG 0.009 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7621 (t0) cc_final: 0.7365 (t0) REVERT: A 243 LEU cc_start: 0.4876 (OUTLIER) cc_final: 0.4591 (pp) REVERT: A 476 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: A 526 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: A 989 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.6700 (mm-40) outliers start: 35 outliers final: 20 residues processed: 128 average time/residue: 1.4626 time to fit residues: 199.4366 Evaluate side-chains 121 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1276 ARG Chi-restraints excluded: chain A residue 1279 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.0040 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 492 GLN A 530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9163 Z= 0.216 Angle : 0.532 8.198 12419 Z= 0.277 Chirality : 0.041 0.166 1419 Planarity : 0.003 0.031 1551 Dihedral : 6.753 80.184 1525 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.74 % Allowed : 15.60 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1123 helix: 1.57 (0.19), residues: 739 sheet: 0.15 (0.54), residues: 74 loop : -1.06 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 314 HIS 0.002 0.001 HIS A 428 PHE 0.022 0.001 PHE A 776 TYR 0.017 0.001 TYR A 337 ARG 0.010 0.001 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7635 (t0) cc_final: 0.7382 (t0) REVERT: A 243 LEU cc_start: 0.4741 (OUTLIER) cc_final: 0.4482 (pp) REVERT: A 476 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: A 521 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 526 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: A 989 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6771 (mm-40) outliers start: 35 outliers final: 25 residues processed: 125 average time/residue: 1.4191 time to fit residues: 188.3895 Evaluate side-chains 125 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1276 ARG Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 0.0000 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 361 GLN A 492 GLN A 530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9163 Z= 0.178 Angle : 0.503 7.601 12419 Z= 0.262 Chirality : 0.040 0.167 1419 Planarity : 0.003 0.037 1551 Dihedral : 6.553 84.279 1525 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.63 % Allowed : 15.71 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1123 helix: 1.69 (0.19), residues: 739 sheet: 0.27 (0.55), residues: 74 loop : -1.05 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 314 HIS 0.002 0.001 HIS A 615 PHE 0.021 0.001 PHE A 776 TYR 0.018 0.001 TYR A 337 ARG 0.010 0.000 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7621 (t0) cc_final: 0.7375 (t0) REVERT: A 243 LEU cc_start: 0.4675 (OUTLIER) cc_final: 0.4415 (pp) REVERT: A 476 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: A 521 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 526 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: A 989 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.6706 (mm-40) REVERT: A 1186 GLU cc_start: 0.7721 (tp30) cc_final: 0.7493 (mp0) outliers start: 34 outliers final: 23 residues processed: 125 average time/residue: 1.4305 time to fit residues: 190.5539 Evaluate side-chains 121 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1276 ARG Chi-restraints excluded: chain A residue 1279 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 79 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 492 GLN A 530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9163 Z= 0.184 Angle : 0.511 7.658 12419 Z= 0.266 Chirality : 0.040 0.169 1419 Planarity : 0.003 0.042 1551 Dihedral : 6.513 85.331 1525 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.74 % Allowed : 16.03 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1123 helix: 1.71 (0.19), residues: 739 sheet: 0.27 (0.55), residues: 74 loop : -1.06 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 314 HIS 0.002 0.001 HIS A1275 PHE 0.021 0.001 PHE A 776 TYR 0.018 0.001 TYR A1037 ARG 0.011 0.000 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7632 (t0) cc_final: 0.7383 (t0) REVERT: A 243 LEU cc_start: 0.4611 (OUTLIER) cc_final: 0.4360 (pp) REVERT: A 476 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8251 (tp30) REVERT: A 526 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: A 989 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.6715 (mm-40) REVERT: A 1186 GLU cc_start: 0.7765 (tp30) cc_final: 0.7527 (mp0) outliers start: 35 outliers final: 25 residues processed: 126 average time/residue: 1.3264 time to fit residues: 178.3417 Evaluate side-chains 122 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1276 ARG Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9163 Z= 0.313 Angle : 0.607 8.737 12419 Z= 0.316 Chirality : 0.044 0.210 1419 Planarity : 0.004 0.038 1551 Dihedral : 7.177 80.321 1525 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.53 % Allowed : 16.99 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1123 helix: 1.28 (0.19), residues: 739 sheet: 0.07 (0.55), residues: 69 loop : -1.14 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 846 HIS 0.003 0.001 HIS A 428 PHE 0.023 0.002 PHE A 776 TYR 0.018 0.002 TYR A1037 ARG 0.011 0.001 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 96 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7619 (t0) cc_final: 0.7372 (t0) REVERT: A 476 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8265 (tp30) REVERT: A 526 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7676 (tp30) REVERT: A 989 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.6944 (mm-40) REVERT: A 1186 GLU cc_start: 0.7762 (tp30) cc_final: 0.7514 (mp0) outliers start: 33 outliers final: 20 residues processed: 123 average time/residue: 1.3915 time to fit residues: 182.1537 Evaluate side-chains 116 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1295 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 107 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9163 Z= 0.191 Angle : 0.533 7.989 12419 Z= 0.277 Chirality : 0.041 0.186 1419 Planarity : 0.003 0.043 1551 Dihedral : 6.751 85.331 1525 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.99 % Allowed : 17.63 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1123 helix: 1.56 (0.19), residues: 740 sheet: 0.21 (0.55), residues: 74 loop : -1.12 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 314 HIS 0.002 0.001 HIS A 428 PHE 0.022 0.001 PHE A 776 TYR 0.018 0.001 TYR A1037 ARG 0.011 0.000 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7603 (t0) cc_final: 0.7345 (t0) REVERT: A 476 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8244 (tp30) REVERT: A 526 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7608 (tp30) REVERT: A 989 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6772 (mm-40) REVERT: A 1186 GLU cc_start: 0.7793 (tp30) cc_final: 0.7546 (mp0) outliers start: 28 outliers final: 22 residues processed: 117 average time/residue: 1.3525 time to fit residues: 168.9992 Evaluate side-chains 114 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9163 Z= 0.349 Angle : 0.644 8.882 12419 Z= 0.335 Chirality : 0.045 0.161 1419 Planarity : 0.004 0.035 1551 Dihedral : 7.272 79.762 1525 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.67 % Allowed : 17.95 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1123 helix: 1.15 (0.18), residues: 739 sheet: -0.00 (0.54), residues: 69 loop : -1.22 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 846 HIS 0.004 0.001 HIS A 428 PHE 0.024 0.002 PHE A 776 TYR 0.017 0.002 TYR A1037 ARG 0.009 0.001 ARG A1050 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7603 (t0) cc_final: 0.7350 (t0) REVERT: A 476 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: A 521 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7473 (mm-30) REVERT: A 526 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7678 (tp30) REVERT: A 554 GLU cc_start: 0.7721 (tp30) cc_final: 0.7413 (tp30) REVERT: A 989 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.6960 (mm-40) REVERT: A 1186 GLU cc_start: 0.7796 (tp30) cc_final: 0.7537 (mp0) outliers start: 25 outliers final: 21 residues processed: 112 average time/residue: 1.3656 time to fit residues: 162.9721 Evaluate side-chains 114 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.0020 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102466 restraints weight = 12739.391| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.26 r_work: 0.3126 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 161 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 249 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9163 Z= 0.158 Angle : 0.514 7.473 12419 Z= 0.267 Chirality : 0.040 0.163 1419 Planarity : 0.003 0.041 1551 Dihedral : 6.569 88.869 1525 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 18.38 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1123 helix: 1.65 (0.19), residues: 740 sheet: 0.22 (0.55), residues: 74 loop : -1.11 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1071 HIS 0.002 0.001 HIS A 615 PHE 0.021 0.001 PHE A 776 TYR 0.019 0.001 TYR A1037 ARG 0.010 0.001 ARG A 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3865.36 seconds wall clock time: 70 minutes 2.16 seconds (4202.16 seconds total)