Starting phenix.real_space_refine on Fri Oct 23 07:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/32ul_59180/10_2026/32ul_59180.cif Found real_map, /net/cci-nas-00/data/ceres_data/32ul_59180/10_2026/32ul_59180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/32ul_59180/10_2026/32ul_59180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/32ul_59180/10_2026/32ul_59180.map" model { file = "/net/cci-nas-00/data/ceres_data/32ul_59180/10_2026/32ul_59180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/32ul_59180/10_2026/32ul_59180.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 5532 2.51 5 N 1529 2.21 5 O 1633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8769 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8737 Classifications: {'peptide': 1088} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1038} Chain breaks: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.82, per 1000 atoms: 0.21 Number of scatterers: 8769 At special positions: 0 Unit cell: (146.642, 127.633, 109.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 3 15.00 Mg 1 11.99 O 1633 8.00 N 1529 7.00 C 5532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 321.1 milliseconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 6 sheets defined 48.5% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 156 through 167 removed outlier: 3.613A pdb=" N THR A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.703A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.573A pdb=" N ARG A 192 " --> pdb=" O CYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.659A pdb=" N VAL A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.894A pdb=" N ALA A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 239 through 258 removed outlier: 4.137A pdb=" N HIS A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.778A pdb=" N MET A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.645A pdb=" N SER A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 312 removed outlier: 3.787A pdb=" N GLU A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 341 through 347 Processing helix chain 'A' and resid 364 through 394 removed outlier: 4.017A pdb=" N HIS A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Proline residue: A 383 - end of helix Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 473 through 480 Processing helix chain 'A' and resid 487 through 495 removed outlier: 4.155A pdb=" N LEU A 493 " --> pdb=" O GLN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 removed outlier: 3.552A pdb=" N VAL A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.668A pdb=" N VAL A 530 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.644A pdb=" N MET A 551 " --> pdb=" O TYR A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.742A pdb=" N LEU A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 639 removed outlier: 3.691A pdb=" N LYS A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 632 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 removed outlier: 4.083A pdb=" N TRP A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.876A pdb=" N GLN A 691 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 699 Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 709 through 740 Processing helix chain 'A' and resid 818 through 822 removed outlier: 3.542A pdb=" N LEU A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 818 through 822' Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 939 through 974 removed outlier: 3.938A pdb=" N MET A 963 " --> pdb=" O SER A 959 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 removed outlier: 3.655A pdb=" N LYS A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1007 through 1011 removed outlier: 3.651A pdb=" N GLU A1010 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1011 " --> pdb=" O ALA A1008 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1007 through 1011' Processing helix chain 'A' and resid 1012 through 1020 removed outlier: 3.649A pdb=" N THR A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1049 Processing helix chain 'A' and resid 1054 through 1062 Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1096 through 1100 Processing helix chain 'A' and resid 1133 through 1148 removed outlier: 3.837A pdb=" N GLU A1148 " --> pdb=" O PHE A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1152 No H-bonds generated for 'chain 'A' and resid 1150 through 1152' Processing helix chain 'A' and resid 1161 through 1170 removed outlier: 3.956A pdb=" N LEU A1170 " --> pdb=" O CYS A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1212 removed outlier: 4.112A pdb=" N LEU A1211 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A1212 " --> pdb=" O GLY A1209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1208 through 1212' Processing helix chain 'A' and resid 1213 through 1222 removed outlier: 4.253A pdb=" N VAL A1219 " --> pdb=" O ASN A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1238 removed outlier: 3.934A pdb=" N LEU A1237 " --> pdb=" O ASN A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1252 removed outlier: 3.636A pdb=" N GLU A1252 " --> pdb=" O HIS A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1282 Processing helix chain 'A' and resid 1336 through 1340 Processing helix chain 'A' and resid 1416 through 1424 removed outlier: 4.159A pdb=" N GLU A1420 " --> pdb=" O CYS A1416 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY A1421 " --> pdb=" O GLY A1417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 468 removed outlier: 3.555A pdb=" N LEU A 453 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET A 505 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE A 412 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLU A 507 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 410 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE A 416 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN A 431 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 677 through 680 removed outlier: 6.352A pdb=" N VAL A 678 " --> pdb=" O GLY A 982 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR A 984 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL A 680 " --> pdb=" O THR A 984 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 983 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 653 " --> pdb=" O ILE A1004 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A1003 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE A1030 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A1005 " --> pdb=" O ILE A1030 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1180 through 1183 removed outlier: 6.965A pdb=" N ILE A1154 " --> pdb=" O ARG A1180 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N HIS A1182 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A1156 " --> pdb=" O HIS A1182 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP A1193 " --> pdb=" O GLY A1227 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TYR A1229 " --> pdb=" O ASP A1193 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A1195 " --> pdb=" O TYR A1229 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE A1231 " --> pdb=" O ILE A1195 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A1197 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE A1112 " --> pdb=" O GLY A1257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1260 through 1261 Processing sheet with id=AA5, first strand: chain 'A' and resid 1347 through 1351 removed outlier: 3.733A pdb=" N GLN A1359 " --> pdb=" O LYS A1350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1401 through 1405 336 hydrogen bonds defined for protein. 933 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: 1.39 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2603 1.33 - 1.45: 1360 1.45 - 1.57: 4868 1.57 - 1.70: 5 1.70 - 1.82: 97 Bond restraints: 8933 Sorted by residual: bond pdb=" CB VAL A1200 " pdb=" CG1 VAL A1200 " ideal model delta sigma weight residual 1.521 1.391 0.130 3.30e-02 9.18e+02 1.55e+01 bond pdb=" N ILE A 823 " pdb=" CA ILE A 823 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.22e-02 6.72e+03 9.09e+00 bond pdb=" N VAL A1181 " pdb=" CA VAL A1181 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.47e+00 bond pdb=" N VAL A1183 " pdb=" CA VAL A1183 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.38e-02 5.25e+03 8.33e+00 bond pdb=" N VAL A1179 " pdb=" CA VAL A1179 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.27e-02 6.20e+03 8.24e+00 ... (remaining 8928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 11803 3.99 - 7.98: 236 7.98 - 11.97: 24 11.97 - 15.96: 1 15.96 - 19.95: 4 Bond angle restraints: 12068 Sorted by residual: angle pdb=" PA ATP A2002 " pdb=" O3A ATP A2002 " pdb=" PB ATP A2002 " ideal model delta sigma weight residual 136.83 128.20 8.63 1.00e+00 1.00e+00 7.45e+01 angle pdb=" N SER A1202 " pdb=" CA SER A1202 " pdb=" C SER A1202 " ideal model delta sigma weight residual 114.16 124.17 -10.01 1.48e+00 4.57e-01 4.57e+01 angle pdb=" N ILE A 838 " pdb=" CA ILE A 838 " pdb=" C ILE A 838 " ideal model delta sigma weight residual 112.43 106.31 6.12 9.20e-01 1.18e+00 4.43e+01 angle pdb=" N VAL A1200 " pdb=" CA VAL A1200 " pdb=" C VAL A1200 " ideal model delta sigma weight residual 109.34 121.49 -12.15 2.08e+00 2.31e-01 3.41e+01 angle pdb=" CA LEU A 666 " pdb=" CB LEU A 666 " pdb=" CG LEU A 666 " ideal model delta sigma weight residual 116.30 136.25 -19.95 3.50e+00 8.16e-02 3.25e+01 ... (remaining 12063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4559 17.97 - 35.93: 704 35.93 - 53.90: 198 53.90 - 71.86: 51 71.86 - 89.82: 17 Dihedral angle restraints: 5529 sinusoidal: 2333 harmonic: 3196 Sorted by residual: dihedral pdb=" CA ASN A1203 " pdb=" C ASN A1203 " pdb=" N GLN A1204 " pdb=" CA GLN A1204 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA VAL A 980 " pdb=" C VAL A 980 " pdb=" N VAL A 981 " pdb=" CA VAL A 981 " ideal model delta harmonic sigma weight residual 180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA GLN A1129 " pdb=" C GLN A1129 " pdb=" N ASN A1130 " pdb=" CA ASN A1130 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 5526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 816 0.057 - 0.115: 400 0.115 - 0.172: 123 0.172 - 0.229: 19 0.229 - 0.286: 6 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CG LEU A 975 " pdb=" CB LEU A 975 " pdb=" CD1 LEU A 975 " pdb=" CD2 LEU A 975 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA HIS A 372 " pdb=" N HIS A 372 " pdb=" C HIS A 372 " pdb=" CB HIS A 372 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU A1196 " pdb=" CB LEU A1196 " pdb=" CD1 LEU A1196 " pdb=" CD2 LEU A1196 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1361 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1243 " 0.021 2.00e-02 2.50e+03 3.00e-02 2.25e+01 pdb=" CG TRP A1243 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP A1243 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TRP A1243 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A1243 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP A1243 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A1243 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1243 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1243 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1243 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1290 " -0.058 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO A1291 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A1291 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1291 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1150 " -0.016 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C LEU A1150 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU A1150 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO A1151 " -0.017 2.00e-02 2.50e+03 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 75 2.63 - 3.20: 7947 3.20 - 3.76: 12994 3.76 - 4.33: 17585 4.33 - 4.90: 29084 Nonbonded interactions: 67685 Sorted by model distance: nonbonded pdb=" OE2 GLU A1007 " pdb="MG MG A2001 " model vdw 2.062 2.170 nonbonded pdb=" O ASN A1116 " pdb=" ND2 ASN A1116 " model vdw 2.178 3.120 nonbonded pdb=" N LYS A1126 " pdb=" N SER A1127 " model vdw 2.291 2.560 nonbonded pdb=" O ASN A 460 " pdb=" OD1 ASN A 460 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLU A1119 " pdb=" N ASN A1203 " model vdw 2.357 3.120 ... (remaining 67680 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: 1.280 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.011 0.130 8933 Z= 0.475 Angle : 1.371 19.945 12068 Z= 0.725 Chirality : 0.071 0.286 1364 Planarity : 0.010 0.088 1551 Dihedral : 19.492 89.825 3451 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.79 % Favored : 91.84 % Rotamer: Outliers : 4.02 % Allowed : 26.53 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.23), residues: 1078 helix: -1.48 (0.22), residues: 431 sheet: -2.04 (0.49), residues: 100 loop : -1.95 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG A 836 TYR 0.050 0.005 TYR A 511 PHE 0.044 0.005 PHE A 461 TRP 0.073 0.011 TRP A1243 HIS 0.020 0.004 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.01129 / 0.47 ( 8933) covalent geometry : angle 1.37138 / 0.72 (12068) hydrogen bonds : bond 0.18621 / 12.07 ( 336) hydrogen bonds : angle 7.06596 / 5.18 ( 933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6542 (tp30) REVERT: A 310 ARG cc_start: 0.3898 (OUTLIER) cc_final: 0.2691 (tpm170) REVERT: A 350 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5987 (mtt180) REVERT: A 456 MET cc_start: 0.8525 (ptm) cc_final: 0.8305 (ptp) REVERT: A 528 GLU cc_start: 0.8045 (pt0) cc_final: 0.7836 (pt0) REVERT: A 599 ASP cc_start: 0.8299 (p0) cc_final: 0.8033 (p0) REVERT: A 640 GLU cc_start: 0.6864 (pm20) cc_final: 0.6533 (mt-10) REVERT: A 671 ASN cc_start: 0.8122 (t0) cc_final: 0.7605 (t0) REVERT: A 699 ASN cc_start: 0.7556 (m110) cc_final: 0.6863 (m-40) REVERT: A 709 MET cc_start: 0.6089 (mmt) cc_final: 0.5195 (mmt) REVERT: A 716 MET cc_start: 0.3637 (mmp) cc_final: 0.3044 (tmm) REVERT: A 719 MET cc_start: 0.6394 (tmm) cc_final: 0.5962 (ptt) REVERT: A 722 MET cc_start: 0.4047 (mmm) cc_final: 0.3331 (tmm) REVERT: A 962 ARG cc_start: 0.6634 (mmm160) cc_final: 0.6279 (mmm160) REVERT: A 963 MET cc_start: 0.8150 (mmt) cc_final: 0.7928 (mmt) REVERT: A 997 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8300 (mtmm) REVERT: A 1062 VAL cc_start: 0.8327 (t) cc_final: 0.8093 (m) REVERT: A 1078 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8454 (mt-10) REVERT: A 1188 GLN cc_start: 0.8780 (tp40) cc_final: 0.8566 (tp40) REVERT: A 1207 LYS cc_start: 0.8498 (tppp) cc_final: 0.8257 (mmmt) REVERT: A 1285 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7969 (mt-10) REVERT: A 1319 MET cc_start: 0.3603 (tpt) cc_final: 0.3060 (mmm) REVERT: A 1381 ARG cc_start: 0.4198 (ttt180) cc_final: 0.2992 (tpp-160) REVERT: A 1385 ARG cc_start: 0.8425 (mmt-90) cc_final: 0.8107 (mmp80) REVERT: A 1407 LYS cc_start: 0.0564 (OUTLIER) cc_final: -0.0045 (mtpp) outliers start: 40 outliers final: 18 residues processed: 168 average time/residue: 0.1175 time to fit residues: 25.6383 Evaluate side-chains 133 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 705 ARG Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1201 ARG Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1407 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 106, 38] chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0020 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 618 GLN A 721 GLN A 969 GLN ** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 GLN A1123 GLN A1128 HIS ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 HIS A1271 HIS ** A1384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.188605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147950 restraints weight = 11219.626| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.92 r_work: 0.3460 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8933 Z= 0.150 Angle : 0.780 15.637 12068 Z= 0.390 Chirality : 0.047 0.181 1364 Planarity : 0.006 0.057 1551 Dihedral : 10.119 66.065 1274 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.92 % Favored : 94.81 % Rotamer: Outliers : 4.62 % Allowed : 22.91 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.25), residues: 1078 helix: -0.33 (0.24), residues: 433 sheet: -1.51 (0.51), residues: 106 loop : -1.61 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1058 TYR 0.019 0.002 TYR A 956 PHE 0.016 0.002 PHE A 461 TRP 0.016 0.003 TRP A1243 HIS 0.006 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8933) covalent geometry : angle 0.78002 / 0.39 (12068) hydrogen bonds : bond 0.04689 / 2.92 ( 336) hydrogen bonds : angle 5.15250 / 3.76 ( 933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 159 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6595 (tp30) REVERT: A 199 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6990 (ptm) REVERT: A 249 SER cc_start: 0.9365 (OUTLIER) cc_final: 0.9146 (p) REVERT: A 310 ARG cc_start: 0.3415 (OUTLIER) cc_final: 0.2308 (tpm170) REVERT: A 389 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7390 (mm) REVERT: A 456 MET cc_start: 0.8476 (ptm) cc_final: 0.8212 (ptp) REVERT: A 489 GLN cc_start: 0.6994 (mm110) cc_final: 0.6748 (mp10) REVERT: A 589 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: A 640 GLU cc_start: 0.6706 (pm20) cc_final: 0.6013 (mt-10) REVERT: A 709 MET cc_start: 0.5117 (mmt) cc_final: 0.4114 (mmt) REVERT: A 710 HIS cc_start: 0.2691 (OUTLIER) cc_final: 0.1263 (m-70) REVERT: A 716 MET cc_start: 0.3417 (mmp) cc_final: 0.2867 (tmm) REVERT: A 719 MET cc_start: 0.6231 (tmm) cc_final: 0.5837 (ptt) REVERT: A 722 MET cc_start: 0.3645 (mmm) cc_final: 0.3054 (tmm) REVERT: A 839 GLU cc_start: 0.7197 (tt0) cc_final: 0.6014 (mm-30) REVERT: A 962 ARG cc_start: 0.6337 (mmm160) cc_final: 0.5786 (mmt180) REVERT: A 977 ASP cc_start: 0.0576 (OUTLIER) cc_final: -0.0408 (p0) REVERT: A 1047 LYS cc_start: 0.8495 (ptmt) cc_final: 0.8203 (ptmm) REVERT: A 1062 VAL cc_start: 0.8300 (t) cc_final: 0.8080 (m) REVERT: A 1123 GLN cc_start: 0.5047 (OUTLIER) cc_final: 0.4743 (tp40) REVERT: A 1188 GLN cc_start: 0.8681 (tp40) cc_final: 0.8359 (tp40) REVERT: A 1201 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7097 (mmm160) REVERT: A 1207 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7723 (mmmt) REVERT: A 1319 MET cc_start: 0.1845 (tpt) cc_final: 0.1335 (mmm) REVERT: A 1336 VAL cc_start: -0.1651 (OUTLIER) cc_final: -0.1948 (t) REVERT: A 1345 GLN cc_start: 0.7716 (mp10) cc_final: 0.7356 (mp10) REVERT: A 1359 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: A 1381 ARG cc_start: 0.3808 (ttt180) cc_final: 0.2629 (tpp-160) REVERT: A 1407 LYS cc_start: 0.0308 (OUTLIER) cc_final: -0.0187 (mtpp) outliers start: 46 outliers final: 16 residues processed: 165 average time/residue: 0.1088 time to fit residues: 24.0675 Evaluate side-chains 136 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1201 ARG Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1407 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [5, 92, 62, 55, 39, 34, 49, 77, 35, 74, 19] chunk 5 optimal weight: 0.0070 chunk 92 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 699 ASN ** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 GLN A1235 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.179243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137527 restraints weight = 11011.411| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.89 r_work: 0.3365 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8933 Z= 0.159 Angle : 0.746 15.633 12068 Z= 0.369 Chirality : 0.047 0.176 1364 Planarity : 0.005 0.046 1551 Dihedral : 8.947 65.669 1253 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 5.53 % Allowed : 23.12 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.25), residues: 1078 helix: 0.03 (0.25), residues: 435 sheet: -1.21 (0.48), residues: 119 loop : -1.60 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 836 TYR 0.017 0.002 TYR A 956 PHE 0.017 0.002 PHE A1056 TRP 0.011 0.002 TRP A 643 HIS 0.008 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 8933) covalent geometry : angle 0.74579 / 0.37 (12068) hydrogen bonds : bond 0.04944 / 3.06 ( 336) hydrogen bonds : angle 4.91224 / 3.58 ( 933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 159 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6428 (tp30) REVERT: A 199 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7661 (ptm) REVERT: A 249 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.9022 (p) REVERT: A 310 ARG cc_start: 0.3382 (OUTLIER) cc_final: 0.2335 (tpm170) REVERT: A 346 HIS cc_start: 0.8242 (m-70) cc_final: 0.7748 (m170) REVERT: A 389 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7460 (mm) REVERT: A 456 MET cc_start: 0.8487 (ptm) cc_final: 0.8136 (ptp) REVERT: A 473 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7563 (mp0) REVERT: A 640 GLU cc_start: 0.6849 (pm20) cc_final: 0.6399 (mt-10) REVERT: A 709 MET cc_start: 0.5154 (mmt) cc_final: 0.4102 (mmt) REVERT: A 710 HIS cc_start: 0.1969 (OUTLIER) cc_final: 0.0447 (m-70) REVERT: A 716 MET cc_start: 0.3501 (mmp) cc_final: 0.3008 (tmm) REVERT: A 719 MET cc_start: 0.6272 (tmm) cc_final: 0.5920 (ptt) REVERT: A 722 MET cc_start: 0.3521 (mmm) cc_final: 0.2749 (tmm) REVERT: A 839 GLU cc_start: 0.6976 (tt0) cc_final: 0.5985 (mm-30) REVERT: A 962 ARG cc_start: 0.6368 (mmm160) cc_final: 0.5801 (mmt180) REVERT: A 1007 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: A 1123 GLN cc_start: 0.4644 (OUTLIER) cc_final: 0.4377 (mp10) REVERT: A 1188 GLN cc_start: 0.8653 (tp40) cc_final: 0.8399 (tp40) REVERT: A 1196 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8786 (mt) REVERT: A 1207 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8113 (mmmt) REVERT: A 1285 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 1319 MET cc_start: 0.2193 (tpt) cc_final: 0.1684 (mmm) REVERT: A 1345 GLN cc_start: 0.7961 (mp10) cc_final: 0.7550 (mp10) REVERT: A 1359 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6641 (mp10) REVERT: A 1381 ARG cc_start: 0.3665 (ttt180) cc_final: 0.2623 (tpp-160) REVERT: A 1407 LYS cc_start: 0.0258 (OUTLIER) cc_final: -0.0178 (mtpp) outliers start: 55 outliers final: 24 residues processed: 160 average time/residue: 0.0934 time to fit residues: 20.3018 Evaluate side-chains 146 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 973 HIS Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1386 CYS Chi-restraints excluded: chain A residue 1407 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [28, 56, 0, 1, 72, 74, 32, 57, 42, 48, 53] chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN A 699 ASN ** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 HIS A1086 HIS A1115 HIS A1235 GLN ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.180113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139797 restraints weight = 11203.790| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.96 r_work: 0.3260 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8933 Z= 0.136 Angle : 0.670 14.598 12068 Z= 0.336 Chirality : 0.045 0.171 1364 Planarity : 0.005 0.045 1551 Dihedral : 8.272 69.405 1246 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 5.63 % Allowed : 22.21 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.25), residues: 1078 helix: 0.36 (0.25), residues: 436 sheet: -0.99 (0.48), residues: 112 loop : -1.42 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1385 TYR 0.013 0.001 TYR A 548 PHE 0.015 0.002 PHE A1056 TRP 0.009 0.002 TRP A 643 HIS 0.005 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 8933) covalent geometry : angle 0.67045 / 0.34 (12068) hydrogen bonds : bond 0.04333 / 2.70 ( 336) hydrogen bonds : angle 4.65027 / 3.38 ( 933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 111 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 159 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6409 (tp30) REVERT: A 249 SER cc_start: 0.9238 (OUTLIER) cc_final: 0.8944 (p) REVERT: A 295 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7524 (mt) REVERT: A 310 ARG cc_start: 0.3269 (OUTLIER) cc_final: 0.2314 (tpm170) REVERT: A 346 HIS cc_start: 0.8348 (m-70) cc_final: 0.7936 (m170) REVERT: A 389 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7216 (mm) REVERT: A 456 MET cc_start: 0.8483 (ptm) cc_final: 0.8143 (ptp) REVERT: A 473 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7487 (mp0) REVERT: A 589 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: A 640 GLU cc_start: 0.7102 (pm20) cc_final: 0.6337 (mt-10) REVERT: A 709 MET cc_start: 0.5067 (mmt) cc_final: 0.4102 (mmt) REVERT: A 710 HIS cc_start: 0.1910 (OUTLIER) cc_final: 0.0761 (m-70) REVERT: A 716 MET cc_start: 0.3591 (mmt) cc_final: 0.2867 (tmm) REVERT: A 719 MET cc_start: 0.6311 (tmm) cc_final: 0.5891 (ptt) REVERT: A 722 MET cc_start: 0.3699 (mmm) cc_final: 0.2843 (tmm) REVERT: A 729 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5183 (pp) REVERT: A 962 ARG cc_start: 0.6557 (mmm160) cc_final: 0.5757 (mmt180) REVERT: A 1123 GLN cc_start: 0.4981 (OUTLIER) cc_final: 0.4646 (mp10) REVERT: A 1188 GLN cc_start: 0.8662 (tp40) cc_final: 0.8355 (tp-100) REVERT: A 1207 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8038 (mmmt) REVERT: A 1319 MET cc_start: 0.2818 (tpt) cc_final: 0.2175 (mmm) REVERT: A 1345 GLN cc_start: 0.7805 (mp10) cc_final: 0.7465 (mp10) REVERT: A 1359 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: A 1381 ARG cc_start: 0.3934 (ttt180) cc_final: 0.2805 (tpp-160) REVERT: A 1407 LYS cc_start: 0.0447 (OUTLIER) cc_final: 0.0015 (mtpp) outliers start: 56 outliers final: 30 residues processed: 156 average time/residue: 0.1018 time to fit residues: 21.3818 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 973 HIS Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1186 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1386 CYS Chi-restraints excluded: chain A residue 1407 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [76, 52, 53, 88, 91, 58, 48, 95, 8, 64, 71] chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 58 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN ** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1050 ASN A1235 GLN ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.177615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136070 restraints weight = 11112.842| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.99 r_work: 0.3374 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8933 Z= 0.132 Angle : 0.646 11.321 12068 Z= 0.324 Chirality : 0.044 0.163 1364 Planarity : 0.005 0.045 1551 Dihedral : 7.948 76.451 1243 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 5.73 % Allowed : 22.71 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1078 helix: 0.51 (0.25), residues: 436 sheet: -0.61 (0.49), residues: 109 loop : -1.29 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1385 TYR 0.014 0.001 TYR A 548 PHE 0.018 0.002 PHE A1117 TRP 0.008 0.001 TRP A 643 HIS 0.006 0.001 HIS A1073 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 8933) covalent geometry : angle 0.64638 / 0.32 (12068) hydrogen bonds : bond 0.04329 / 2.69 ( 336) hydrogen bonds : angle 4.54546 / 3.29 ( 933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 108 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6564 (tp30) REVERT: A 249 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8960 (p) REVERT: A 295 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7547 (mt) REVERT: A 310 ARG cc_start: 0.3070 (OUTLIER) cc_final: 0.2236 (tpm170) REVERT: A 389 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7253 (mm) REVERT: A 421 CYS cc_start: 0.8260 (p) cc_final: 0.8014 (m) REVERT: A 456 MET cc_start: 0.8517 (ptm) cc_final: 0.8172 (ptp) REVERT: A 473 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7600 (mp0) REVERT: A 589 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: A 709 MET cc_start: 0.4981 (mmt) cc_final: 0.3956 (mmt) REVERT: A 710 HIS cc_start: 0.1939 (OUTLIER) cc_final: 0.0722 (m-70) REVERT: A 716 MET cc_start: 0.2963 (mmt) cc_final: 0.2379 (tmm) REVERT: A 719 MET cc_start: 0.6326 (tmm) cc_final: 0.5982 (ptt) REVERT: A 722 MET cc_start: 0.3705 (mmm) cc_final: 0.2898 (tmm) REVERT: A 729 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5149 (pp) REVERT: A 962 ARG cc_start: 0.6451 (mmm160) cc_final: 0.6002 (mmt180) REVERT: A 965 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.5725 (mt-10) REVERT: A 967 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7952 (mmm-85) REVERT: A 1007 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: A 1188 GLN cc_start: 0.8586 (tp40) cc_final: 0.8194 (tp40) REVERT: A 1207 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8017 (mmmt) REVERT: A 1252 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7125 (mm-30) REVERT: A 1273 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 1319 MET cc_start: 0.2756 (tpt) cc_final: 0.2119 (mmm) REVERT: A 1345 GLN cc_start: 0.7858 (mp10) cc_final: 0.7479 (mp10) REVERT: A 1358 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6075 (pm20) REVERT: A 1359 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: A 1379 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7777 (t) REVERT: A 1381 ARG cc_start: 0.3843 (ttt180) cc_final: 0.2842 (tpp-160) REVERT: A 1385 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7637 (mmp80) REVERT: A 1407 LYS cc_start: 0.0491 (OUTLIER) cc_final: 0.0078 (mtpp) outliers start: 57 outliers final: 33 residues processed: 154 average time/residue: 0.1031 time to fit residues: 21.2326 Evaluate side-chains 147 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 99 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 973 HIS Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1047 LYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1186 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1358 GLU Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1379 SER Chi-restraints excluded: chain A residue 1386 CYS Chi-restraints excluded: chain A residue 1407 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [71, 12, 1, 53, 5, 92, 97, 45, 80, 102, 73] chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.182227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.142939 restraints weight = 11007.280| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.20 r_work: 0.3287 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8933 Z= 0.149 Angle : 0.665 10.860 12068 Z= 0.334 Chirality : 0.045 0.173 1364 Planarity : 0.005 0.044 1551 Dihedral : 7.806 86.002 1240 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 6.23 % Allowed : 22.31 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.25), residues: 1078 helix: 0.50 (0.25), residues: 434 sheet: -0.56 (0.53), residues: 97 loop : -1.30 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 836 TYR 0.016 0.001 TYR A 548 PHE 0.019 0.002 PHE A1117 TRP 0.010 0.001 TRP A 643 HIS 0.006 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 8933) covalent geometry : angle 0.66536 / 0.33 (12068) hydrogen bonds : bond 0.04550 / 2.83 ( 336) hydrogen bonds : angle 4.54590 / 3.29 ( 933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 111 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 159 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6579 (tp30) REVERT: A 249 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8982 (p) REVERT: A 295 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7591 (mt) REVERT: A 310 ARG cc_start: 0.3190 (OUTLIER) cc_final: 0.2271 (tpm170) REVERT: A 389 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7257 (mm) REVERT: A 408 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7523 (mt) REVERT: A 421 CYS cc_start: 0.8301 (p) cc_final: 0.8047 (m) REVERT: A 456 MET cc_start: 0.8531 (ptm) cc_final: 0.8209 (ptp) REVERT: A 459 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7501 (p0) REVERT: A 460 ASN cc_start: 0.7255 (t0) cc_final: 0.6951 (t0) REVERT: A 473 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7639 (mp0) REVERT: A 640 GLU cc_start: 0.7439 (pt0) cc_final: 0.7225 (pt0) REVERT: A 709 MET cc_start: 0.5010 (mmt) cc_final: 0.3979 (mmt) REVERT: A 710 HIS cc_start: 0.2043 (OUTLIER) cc_final: 0.0824 (m-70) REVERT: A 716 MET cc_start: 0.3466 (mmt) cc_final: 0.2833 (tmm) REVERT: A 719 MET cc_start: 0.6418 (tmm) cc_final: 0.6111 (ptt) REVERT: A 722 MET cc_start: 0.3883 (mmm) cc_final: 0.3071 (tmm) REVERT: A 729 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5051 (pp) REVERT: A 965 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: A 967 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.8025 (mmm-85) REVERT: A 1007 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: A 1078 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: A 1188 GLN cc_start: 0.8621 (tp40) cc_final: 0.8225 (tp40) REVERT: A 1252 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7208 (mm-30) REVERT: A 1273 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8315 (mp) REVERT: A 1319 MET cc_start: 0.2829 (tpt) cc_final: 0.2171 (mmm) REVERT: A 1345 GLN cc_start: 0.8012 (mp10) cc_final: 0.7653 (mp10) REVERT: A 1358 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6100 (pm20) REVERT: A 1381 ARG cc_start: 0.3804 (ttt180) cc_final: 0.2875 (tpp-160) REVERT: A 1407 LYS cc_start: 0.0481 (OUTLIER) cc_final: 0.0085 (mtpp) outliers start: 62 outliers final: 33 residues processed: 161 average time/residue: 0.1147 time to fit residues: 24.4796 Evaluate side-chains 150 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 103 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 973 HIS Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1186 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1358 GLU Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1369 ASP Chi-restraints excluded: chain A residue 1386 CYS Chi-restraints excluded: chain A residue 1407 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [43, 95, 7, 103, 77, 14, 20, 69, 55, 97, 72] chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 0.0270 chunk 7 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 0.0370 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 GLN ** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 GLN A1235 GLN ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.179338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138655 restraints weight = 11131.057| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.14 r_work: 0.3281 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8933 Z= 0.111 Angle : 0.613 10.185 12068 Z= 0.307 Chirality : 0.043 0.152 1364 Planarity : 0.004 0.045 1551 Dihedral : 7.190 69.568 1240 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 5.03 % Allowed : 23.72 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.26), residues: 1078 helix: 0.75 (0.26), residues: 434 sheet: -0.48 (0.53), residues: 97 loop : -1.15 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 704 TYR 0.012 0.001 TYR A 548 PHE 0.014 0.001 PHE A1056 TRP 0.006 0.001 TRP A 442 HIS 0.010 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 8933) covalent geometry : angle 0.61304 / 0.31 (12068) hydrogen bonds : bond 0.03878 / 2.47 ( 336) hydrogen bonds : angle 4.41512 / 3.19 ( 933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.6983 (tp30) cc_final: 0.6646 (mp0) REVERT: A 295 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7708 (mt) REVERT: A 310 ARG cc_start: 0.3103 (OUTLIER) cc_final: 0.2466 (tpp-160) REVERT: A 389 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7102 (mm) REVERT: A 408 ILE cc_start: 0.7965 (pt) cc_final: 0.7523 (mt) REVERT: A 421 CYS cc_start: 0.8261 (p) cc_final: 0.7926 (m) REVERT: A 456 MET cc_start: 0.8602 (ptm) cc_final: 0.8232 (ptp) REVERT: A 459 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7352 (p0) REVERT: A 460 ASN cc_start: 0.7279 (t0) cc_final: 0.6937 (t0) REVERT: A 473 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7560 (mp0) REVERT: A 640 GLU cc_start: 0.7192 (pt0) cc_final: 0.6978 (pt0) REVERT: A 709 MET cc_start: 0.4859 (mmt) cc_final: 0.3845 (mmt) REVERT: A 710 HIS cc_start: 0.2193 (OUTLIER) cc_final: 0.0839 (m-70) REVERT: A 716 MET cc_start: 0.3239 (mmt) cc_final: 0.2488 (tmm) REVERT: A 719 MET cc_start: 0.6591 (tmm) cc_final: 0.6288 (ptt) REVERT: A 722 MET cc_start: 0.3826 (mmm) cc_final: 0.3055 (tmm) REVERT: A 729 LEU cc_start: 0.5596 (OUTLIER) cc_final: 0.5044 (pp) REVERT: A 965 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: A 1007 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: A 1188 GLN cc_start: 0.8646 (tp40) cc_final: 0.8369 (tp40) REVERT: A 1207 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7894 (mmmt) REVERT: A 1273 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 1319 MET cc_start: 0.2586 (tpt) cc_final: 0.2122 (mmm) REVERT: A 1345 GLN cc_start: 0.7993 (mp10) cc_final: 0.7589 (mp10) REVERT: A 1358 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.5857 (pm20) REVERT: A 1381 ARG cc_start: 0.3850 (ttt180) cc_final: 0.2970 (tpp-160) REVERT: A 1407 LYS cc_start: 0.0716 (OUTLIER) cc_final: 0.0196 (mtpp) outliers start: 50 outliers final: 31 residues processed: 146 average time/residue: 0.0973 time to fit residues: 19.2827 Evaluate side-chains 145 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 973 HIS Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1186 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1358 GLU Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1386 CYS Chi-restraints excluded: chain A residue 1407 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [87, 107, 6, 18, 11, 81, 49, 80, 68, 42, 67] chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 80 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 67 optimal weight: 0.3980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.179669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139503 restraints weight = 11074.549| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.16 r_work: 0.3405 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8933 Z= 0.103 Angle : 0.594 11.840 12068 Z= 0.294 Chirality : 0.043 0.143 1364 Planarity : 0.004 0.044 1551 Dihedral : 6.639 70.514 1238 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 4.72 % Allowed : 23.92 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.26), residues: 1078 helix: 0.91 (0.26), residues: 434 sheet: -0.15 (0.56), residues: 90 loop : -1.02 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1304 TYR 0.013 0.001 TYR A 342 PHE 0.013 0.001 PHE A1056 TRP 0.006 0.001 TRP A 442 HIS 0.009 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 8933) covalent geometry : angle 0.59392 / 0.29 (12068) hydrogen bonds : bond 0.03607 / 2.31 ( 336) hydrogen bonds : angle 4.32037 / 3.14 ( 933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.7164 (tp30) cc_final: 0.6888 (mp0) REVERT: A 295 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7751 (mt) REVERT: A 310 ARG cc_start: 0.3627 (OUTLIER) cc_final: 0.2589 (tpm170) REVERT: A 389 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7104 (mm) REVERT: A 408 ILE cc_start: 0.7985 (pt) cc_final: 0.7516 (mt) REVERT: A 421 CYS cc_start: 0.8404 (p) cc_final: 0.7899 (m) REVERT: A 456 MET cc_start: 0.8631 (ptm) cc_final: 0.8254 (ptp) REVERT: A 459 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7344 (p0) REVERT: A 460 ASN cc_start: 0.7205 (t0) cc_final: 0.6913 (t0) REVERT: A 473 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7567 (mp0) REVERT: A 659 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7555 (m-40) REVERT: A 709 MET cc_start: 0.4433 (mmt) cc_final: 0.3452 (mmt) REVERT: A 710 HIS cc_start: 0.2420 (OUTLIER) cc_final: 0.1299 (m-70) REVERT: A 716 MET cc_start: 0.2752 (mmt) cc_final: 0.2223 (tmm) REVERT: A 722 MET cc_start: 0.4109 (mmm) cc_final: 0.3392 (tmm) REVERT: A 729 LEU cc_start: 0.5601 (OUTLIER) cc_final: 0.5045 (pp) REVERT: A 965 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: A 1007 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8286 (mt-10) REVERT: A 1170 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8524 (mt) REVERT: A 1188 GLN cc_start: 0.8556 (tp40) cc_final: 0.8287 (tp40) REVERT: A 1207 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7995 (mmmt) REVERT: A 1273 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 1301 VAL cc_start: 0.7533 (t) cc_final: 0.7203 (p) REVERT: A 1319 MET cc_start: 0.2710 (tpt) cc_final: 0.2086 (tpp) REVERT: A 1345 GLN cc_start: 0.7900 (mp10) cc_final: 0.7522 (mp10) REVERT: A 1358 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.5970 (pm20) REVERT: A 1381 ARG cc_start: 0.3731 (ttt180) cc_final: 0.3002 (tpp-160) outliers start: 47 outliers final: 24 residues processed: 145 average time/residue: 0.0984 time to fit residues: 19.1661 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1186 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1358 GLU Chi-restraints excluded: chain A residue 1386 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [89, 97, 20, 67, 9, 45, 102, 73, 22, 47, 15] chunk 89 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 0.0770 chunk 15 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 HIS A 491 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.176770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136318 restraints weight = 11057.600| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.06 r_work: 0.3335 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8933 Z= 0.136 Angle : 0.658 13.932 12068 Z= 0.322 Chirality : 0.045 0.168 1364 Planarity : 0.005 0.052 1551 Dihedral : 6.685 69.842 1229 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 4.42 % Allowed : 24.12 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 1078 helix: 0.85 (0.26), residues: 434 sheet: -0.16 (0.56), residues: 90 loop : -1.09 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 967 TYR 0.018 0.001 TYR A 548 PHE 0.015 0.002 PHE A1056 TRP 0.009 0.001 TRP A 643 HIS 0.008 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 8933) covalent geometry : angle 0.65779 / 0.32 (12068) hydrogen bonds : bond 0.04315 / 2.70 ( 336) hydrogen bonds : angle 4.39782 / 3.19 ( 933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 288 GLU cc_start: 0.7127 (tp30) cc_final: 0.6778 (mp0) REVERT: A 295 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7762 (mt) REVERT: A 319 TYR cc_start: 0.7446 (t80) cc_final: 0.7205 (t80) REVERT: A 389 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7187 (mm) REVERT: A 408 ILE cc_start: 0.7994 (pt) cc_final: 0.7630 (mt) REVERT: A 421 CYS cc_start: 0.8244 (p) cc_final: 0.7926 (m) REVERT: A 456 MET cc_start: 0.8533 (ptm) cc_final: 0.8195 (ptp) REVERT: A 459 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7381 (p0) REVERT: A 460 ASN cc_start: 0.7404 (t0) cc_final: 0.7112 (t0) REVERT: A 473 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7601 (mp0) REVERT: A 709 MET cc_start: 0.3119 (mmt) cc_final: 0.2508 (mmt) REVERT: A 722 MET cc_start: 0.4121 (mmm) cc_final: 0.3460 (tmm) REVERT: A 729 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.4998 (pp) REVERT: A 965 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: A 1007 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: A 1207 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7946 (mmmt) REVERT: A 1273 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 1319 MET cc_start: 0.2975 (tpt) cc_final: 0.2540 (tpp) REVERT: A 1345 GLN cc_start: 0.7935 (mp10) cc_final: 0.7557 (mp10) REVERT: A 1358 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6323 (pm20) REVERT: A 1359 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: A 1381 ARG cc_start: 0.3810 (ttt180) cc_final: 0.2909 (tpp-160) outliers start: 44 outliers final: 28 residues processed: 142 average time/residue: 0.1069 time to fit residues: 20.2527 Evaluate side-chains 145 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1186 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1358 GLU Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1371 CYS Chi-restraints excluded: chain A residue 1386 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [90, 30, 66, 9, 45, 25, 75, 3, 65, 23, 41] chunk 90 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1235 GLN A1418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140305 restraints weight = 10896.442| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.98 r_work: 0.3205 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8933 Z= 0.151 Angle : 0.688 14.495 12068 Z= 0.336 Chirality : 0.046 0.174 1364 Planarity : 0.005 0.050 1551 Dihedral : 6.520 72.404 1223 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.78 % Rotamer: Outliers : 4.32 % Allowed : 24.52 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.25), residues: 1078 helix: 0.74 (0.25), residues: 433 sheet: -0.17 (0.55), residues: 90 loop : -1.12 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 712 TYR 0.017 0.001 TYR A 548 PHE 0.016 0.002 PHE A1056 TRP 0.009 0.002 TRP A 643 HIS 0.008 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 ( 8933) covalent geometry : angle 0.68828 / 0.34 (12068) hydrogen bonds : bond 0.04529 / 2.83 ( 336) hydrogen bonds : angle 4.50047 / 3.25 ( 933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 SER cc_start: 0.9127 (OUTLIER) cc_final: 0.8771 (p) REVERT: A 288 GLU cc_start: 0.7088 (tp30) cc_final: 0.6738 (mp0) REVERT: A 295 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7621 (mt) REVERT: A 319 TYR cc_start: 0.7479 (t80) cc_final: 0.7268 (t80) REVERT: A 389 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7051 (mm) REVERT: A 408 ILE cc_start: 0.7998 (pt) cc_final: 0.7633 (mt) REVERT: A 421 CYS cc_start: 0.8235 (p) cc_final: 0.7879 (m) REVERT: A 456 MET cc_start: 0.8483 (ptm) cc_final: 0.8115 (ptp) REVERT: A 459 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7198 (p0) REVERT: A 460 ASN cc_start: 0.7450 (t0) cc_final: 0.7059 (t0) REVERT: A 473 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7540 (mp0) REVERT: A 599 ASP cc_start: 0.8164 (p0) cc_final: 0.7947 (p0) REVERT: A 709 MET cc_start: 0.3476 (mmt) cc_final: 0.2765 (mmt) REVERT: A 722 MET cc_start: 0.4296 (mmm) cc_final: 0.3542 (tmm) REVERT: A 965 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 1007 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: A 1207 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7961 (mmmt) REVERT: A 1273 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 1319 MET cc_start: 0.3580 (tpt) cc_final: 0.3135 (tpp) REVERT: A 1345 GLN cc_start: 0.8020 (mp10) cc_final: 0.7662 (mp10) REVERT: A 1358 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6431 (pm20) REVERT: A 1359 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6780 (pm20) REVERT: A 1381 ARG cc_start: 0.4084 (ttt180) cc_final: 0.3165 (tpp-160) outliers start: 43 outliers final: 28 residues processed: 143 average time/residue: 0.1081 time to fit residues: 20.7389 Evaluate side-chains 147 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 965 GLU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1186 LYS Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1358 GLU Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1371 CYS Chi-restraints excluded: chain A residue 1386 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [55, 41, 31, 36, 59, 0, 3, 52, 72, 77, 27] chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.176691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136086 restraints weight = 10878.682| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.98 r_work: 0.3308 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8933 Z= 0.149 Angle : 0.690 14.308 12068 Z= 0.336 Chirality : 0.046 0.172 1364 Planarity : 0.005 0.051 1551 Dihedral : 6.489 71.241 1223 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 4.32 % Allowed : 24.42 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1078 helix: 0.70 (0.25), residues: 433 sheet: -0.18 (0.56), residues: 90 loop : -1.14 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 967 TYR 0.016 0.001 TYR A 548 PHE 0.016 0.002 PHE A1056 TRP 0.007 0.002 TRP A 643 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 8933) covalent geometry : angle 0.68980 / 0.34 (12068) hydrogen bonds : bond 0.04527 / 2.84 ( 336) hydrogen bonds : angle 4.51644 / 3.24 ( 933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.12 seconds wall clock time: 41 minutes 39.16 seconds (2499.16 seconds total)