Starting phenix.real_space_refine on Wed Apr 10 02:27:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/04_2024/7q2x_13783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/04_2024/7q2x_13783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/04_2024/7q2x_13783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/04_2024/7q2x_13783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/04_2024/7q2x_13783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/04_2024/7q2x_13783_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 76 5.49 5 Mg 2 5.21 5 S 91 5.16 5 Be 2 3.05 5 C 11373 2.51 5 N 3057 2.21 5 O 3633 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1113": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3413 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 1 Chain: "B" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3102 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2279 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 283} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 7906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7906 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 966} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 756 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "G" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.95, per 1000 atoms: 0.55 Number of scatterers: 18240 At special positions: 0 Unit cell: (121.98, 147.66, 161.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 91 16.00 P 76 15.00 Mg 2 11.99 F 6 9.00 O 3633 8.00 N 3057 7.00 C 11373 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D1059 " - pdb=" SG CYS D1071 " distance=2.88 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.38 Conformation dependent library (CDL) restraints added in 3.1 seconds 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 9 sheets defined 60.2% alpha, 6.7% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 8.98 Creating SS restraints... Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.929A pdb=" N LEU A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.870A pdb=" N VAL A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.623A pdb=" N ALA A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 227 Proline residue: A 205 - end of helix removed outlier: 3.985A pdb=" N ARG A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 977 removed outlier: 4.074A pdb=" N LYS A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1047 removed outlier: 3.835A pdb=" N GLU A1027 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1086 through 1103 Processing helix chain 'A' and resid 1120 through 1131 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.925A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 209 Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 335 through 349 removed outlier: 4.302A pdb=" N LEU B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1286 Processing helix chain 'B' and resid 1301 through 1304 No H-bonds generated for 'chain 'B' and resid 1301 through 1304' Processing helix chain 'B' and resid 1325 through 1342 Processing helix chain 'B' and resid 1359 through 1371 Processing helix chain 'B' and resid 1385 through 1389 Processing helix chain 'C' and resid 23 through 40 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 72 through 105 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 300 through 310 removed outlier: 4.004A pdb=" N ARG C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 322 removed outlier: 4.425A pdb=" N ASP C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 668 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 705 through 710 removed outlier: 3.718A pdb=" N ASP C 710 " --> pdb=" O ASP C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 726 Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 27 through 40 removed outlier: 4.151A pdb=" N VAL D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 51 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 67 through 91 Processing helix chain 'D' and resid 105 through 127 Processing helix chain 'D' and resid 154 through 176 Processing helix chain 'D' and resid 186 through 205 removed outlier: 3.545A pdb=" N PHE D 196 " --> pdb=" O PHE D 192 " (cutoff:3.500A) Proline residue: D 199 - end of helix removed outlier: 3.805A pdb=" N GLU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 211 Processing helix chain 'D' and resid 213 through 229 Processing helix chain 'D' and resid 235 through 246 Processing helix chain 'D' and resid 251 through 263 Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 289 through 304 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 313 through 321 removed outlier: 4.006A pdb=" N THR D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 344 removed outlier: 3.577A pdb=" N ALA D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 353 through 367 removed outlier: 3.748A pdb=" N PHE D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 394 through 408 removed outlier: 3.970A pdb=" N LYS D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 441 through 456 Processing helix chain 'D' and resid 518 through 551 Processing helix chain 'D' and resid 556 through 571 Processing helix chain 'D' and resid 577 through 587 removed outlier: 3.851A pdb=" N HIS D 586 " --> pdb=" O LYS D 582 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D 587 " --> pdb=" O LYS D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 611 Processing helix chain 'D' and resid 621 through 637 Processing helix chain 'D' and resid 641 through 656 Processing helix chain 'D' and resid 663 through 675 removed outlier: 4.007A pdb=" N ALA D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 713 removed outlier: 3.851A pdb=" N ALA D 713 " --> pdb=" O MET D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 719 Processing helix chain 'D' and resid 722 through 728 Processing helix chain 'D' and resid 732 through 736 removed outlier: 3.757A pdb=" N LYS D 736 " --> pdb=" O ALA D 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 732 through 736' Processing helix chain 'D' and resid 738 through 749 Processing helix chain 'D' and resid 765 through 780 removed outlier: 4.450A pdb=" N VAL D 770 " --> pdb=" O GLU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 802 removed outlier: 3.665A pdb=" N TYR D 789 " --> pdb=" O ASN D 786 " (cutoff:3.500A) Proline residue: D 790 - end of helix removed outlier: 4.544A pdb=" N GLU D 793 " --> pdb=" O PRO D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 806 through 820 Processing helix chain 'D' and resid 839 through 874 removed outlier: 3.554A pdb=" N GLU D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 922 Processing helix chain 'D' and resid 933 through 945 Proline residue: D 938 - end of helix Processing helix chain 'D' and resid 947 through 950 No H-bonds generated for 'chain 'D' and resid 947 through 950' Processing helix chain 'D' and resid 953 through 967 Processing helix chain 'D' and resid 971 through 986 Proline residue: D 979 - end of helix Processing helix chain 'D' and resid 991 through 1006 Processing helix chain 'D' and resid 1009 through 1012 No H-bonds generated for 'chain 'D' and resid 1009 through 1012' Processing helix chain 'D' and resid 1015 through 1023 Processing helix chain 'D' and resid 1028 through 1043 Processing helix chain 'D' and resid 1053 through 1061 removed outlier: 3.826A pdb=" N CYS D1059 " --> pdb=" O GLU D1055 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU D1060 " --> pdb=" O MET D1056 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP D1061 " --> pdb=" O ALA D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1065 through 1077 removed outlier: 4.285A pdb=" N MET D1070 " --> pdb=" O GLY D1066 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N CYS D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1099 removed outlier: 4.055A pdb=" N ALA D1084 " --> pdb=" O LYS D1081 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE D1085 " --> pdb=" O ASP D1082 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE D1090 " --> pdb=" O ASN D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1117 removed outlier: 3.853A pdb=" N LYS D1109 " --> pdb=" O GLU D1105 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE D1117 " --> pdb=" O PHE D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1123 through 1136 removed outlier: 3.814A pdb=" N ARG D1136 " --> pdb=" O VAL D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1146 Processing helix chain 'D' and resid 1149 through 1153 Processing helix chain 'D' and resid 1159 through 1167 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.975A pdb=" N VAL A 82 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 6 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A 80 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 8 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER A 78 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR A 115 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1165 through 1169 Processing sheet with id= C, first strand: chain 'A' and resid 1051 through 1057 Processing sheet with id= D, first strand: chain 'B' and resid 153 through 156 Processing sheet with id= E, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= F, first strand: chain 'B' and resid 1403 through 1410 removed outlier: 7.572A pdb=" N PHE B 180 " --> pdb=" O GLN B1393 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N VAL B1395 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 182 " --> pdb=" O VAL B1395 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL B1397 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL B 184 " --> pdb=" O VAL B1397 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N LYS B1399 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE B1378 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL B 183 " --> pdb=" O PHE B1378 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B1380 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLY B 185 " --> pdb=" O VAL B1380 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= H, first strand: chain 'B' and resid 1290 through 1295 Processing sheet with id= I, first strand: chain 'C' and resid 730 through 733 934 hydrogen bonds defined for protein. 2649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 9.00 Time building geometry restraints manager: 7.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3160 1.33 - 1.45: 4673 1.45 - 1.57: 10517 1.57 - 1.69: 148 1.69 - 1.81: 153 Bond restraints: 18651 Sorted by residual: bond pdb=" BE BEF A2002 " pdb=" F2 BEF A2002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" BE BEF B2002 " pdb=" F2 BEF B2002 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" BE BEF B2002 " pdb=" F1 BEF B2002 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.59e+00 ... (remaining 18646 not shown) Histogram of bond angle deviations from ideal: 99.69 - 107.00: 794 107.00 - 114.31: 11230 114.31 - 121.61: 9472 121.61 - 128.92: 3797 128.92 - 136.23: 136 Bond angle restraints: 25429 Sorted by residual: angle pdb=" F2 BEF A2002 " pdb=" BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 119.96 107.49 12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" F2 BEF B2002 " pdb=" BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 119.96 107.58 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N PRO A 158 " pdb=" CA PRO A 158 " pdb=" CB PRO A 158 " ideal model delta sigma weight residual 103.30 99.74 3.56 1.12e+00 7.97e-01 1.01e+01 angle pdb=" F1 BEF A2002 " pdb=" BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 120.12 110.99 9.13 3.00e+00 1.11e-01 9.26e+00 angle pdb=" F1 BEF B2002 " pdb=" BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 120.12 110.99 9.13 3.00e+00 1.11e-01 9.25e+00 ... (remaining 25424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 10878 35.96 - 71.93: 442 71.93 - 107.89: 19 107.89 - 143.85: 1 143.85 - 179.82: 3 Dihedral angle restraints: 11343 sinusoidal: 5196 harmonic: 6147 Sorted by residual: dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 101.82 -161.81 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP B2001 " pdb=" O3A ADP B2001 " pdb=" PA ADP B2001 " pdb=" PB ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 85.28 -145.28 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP B2001 " pdb=" O3A ADP B2001 " pdb=" PB ADP B2001 " pdb=" PA ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 69.77 -129.78 1 2.00e+01 2.50e-03 3.94e+01 ... (remaining 11340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2057 0.032 - 0.063: 625 0.063 - 0.095: 195 0.095 - 0.127: 80 0.127 - 0.159: 6 Chirality restraints: 2963 Sorted by residual: chirality pdb=" CA THR D 186 " pdb=" N THR D 186 " pdb=" C THR D 186 " pdb=" CB THR D 186 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE C 731 " pdb=" N ILE C 731 " pdb=" C ILE C 731 " pdb=" CB ILE C 731 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2960 not shown) Planarity restraints: 2951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 305 " 0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO D 306 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO D 306 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 306 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 312 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO B 313 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B1345 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO B1346 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B1346 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1346 " -0.028 5.00e-02 4.00e+02 ... (remaining 2948 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 154 2.61 - 3.18: 15992 3.18 - 3.75: 29288 3.75 - 4.33: 38824 4.33 - 4.90: 63004 Nonbonded interactions: 147262 Sorted by model distance: nonbonded pdb=" F1 BEF B2002 " pdb="MG MG B2003 " model vdw 2.035 2.120 nonbonded pdb=" O2B ADP A2001 " pdb="MG MG A2003 " model vdw 2.063 2.170 nonbonded pdb=" OG SER B 192 " pdb="MG MG B2003 " model vdw 2.085 2.170 nonbonded pdb=" OE1 GLN B 302 " pdb="MG MG B2003 " model vdw 2.133 2.170 nonbonded pdb=" OG SER A 39 " pdb="MG MG A2003 " model vdw 2.143 2.170 ... (remaining 147257 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: 0.200 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: 0.020 Extract box with map and model: 2.020 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 57.480 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 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 : 0.002 0.084 18651 Z= 0.144 Angle : 0.546 12.467 25429 Z= 0.285 Chirality : 0.037 0.159 2963 Planarity : 0.004 0.098 2951 Dihedral : 17.519 179.817 7320 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.19), residues: 2054 helix: 2.71 (0.15), residues: 1260 sheet: 1.48 (0.39), residues: 180 loop : -0.44 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1033 HIS 0.002 0.000 HIS B 235 PHE 0.022 0.001 PHE B1308 TYR 0.012 0.001 TYR D 655 ARG 0.008 0.000 ARG B1384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 438 time to evaluate : 1.960 Fit side-chains REVERT: A 107 VAL cc_start: 0.8294 (p) cc_final: 0.8072 (p) REVERT: A 1003 MET cc_start: 0.7791 (mtp) cc_final: 0.7568 (mtm) REVERT: A 1148 MET cc_start: 0.7876 (tpp) cc_final: 0.7640 (tpp) REVERT: B 331 ILE cc_start: 0.7849 (mp) cc_final: 0.7637 (mp) REVERT: B 1327 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6303 (mt-10) REVERT: B 1388 PHE cc_start: 0.7183 (p90) cc_final: 0.6825 (p90) REVERT: C 70 ILE cc_start: 0.7947 (pt) cc_final: 0.7714 (mt) REVERT: D 244 LEU cc_start: 0.7011 (tp) cc_final: 0.6658 (tp) REVERT: D 413 LEU cc_start: 0.7255 (tp) cc_final: 0.7005 (tp) REVERT: D 555 ASN cc_start: 0.7259 (t0) cc_final: 0.7007 (t0) REVERT: D 558 GLU cc_start: 0.6871 (tt0) cc_final: 0.6583 (tt0) REVERT: D 748 LEU cc_start: 0.8689 (tp) cc_final: 0.8264 (tp) REVERT: D 964 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6408 (mt-10) REVERT: D 1077 GLU cc_start: 0.6307 (tm-30) cc_final: 0.6023 (tm-30) outliers start: 2 outliers final: 0 residues processed: 438 average time/residue: 1.3320 time to fit residues: 651.9645 Evaluate side-chains 389 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 106 GLN B 171 GLN B 266 ASN B 307 ASN C 307 ASN C 653 ASN C 725 ASN C 738 ASN D 70 GLN D 83 ASN D 163 GLN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 GLN D 852 GLN D1062 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18651 Z= 0.361 Angle : 0.692 9.312 25429 Z= 0.361 Chirality : 0.044 0.193 2963 Planarity : 0.005 0.065 2951 Dihedral : 18.669 176.208 3085 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.31 % Allowed : 12.67 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.18), residues: 2054 helix: 2.15 (0.14), residues: 1266 sheet: 1.12 (0.39), residues: 183 loop : -0.61 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1077 HIS 0.009 0.001 HIS D1024 PHE 0.029 0.003 PHE B 180 TYR 0.026 0.002 TYR D 529 ARG 0.009 0.001 ARG D 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 529 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7855 (mtp-110) cc_final: 0.7162 (mtp180) REVERT: A 228 GLU cc_start: 0.6471 (mp0) cc_final: 0.6098 (mp0) REVERT: A 1083 GLU cc_start: 0.7164 (pt0) cc_final: 0.6782 (pt0) REVERT: A 1115 ASP cc_start: 0.8110 (p0) cc_final: 0.7859 (p0) REVERT: A 1131 LYS cc_start: 0.8296 (tttp) cc_final: 0.8084 (tttm) REVERT: A 1157 ARG cc_start: 0.7054 (mtp-110) cc_final: 0.6813 (mtp85) REVERT: B 207 ASN cc_start: 0.7444 (t0) cc_final: 0.7241 (t0) REVERT: B 234 VAL cc_start: 0.8648 (m) cc_final: 0.8409 (t) REVERT: B 1275 SER cc_start: 0.8078 (m) cc_final: 0.7872 (m) REVERT: B 1318 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7439 (mtp85) REVERT: B 1321 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8190 (p) REVERT: B 1327 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7301 (mt-10) REVERT: C 43 ILE cc_start: 0.7647 (mt) cc_final: 0.7439 (mt) REVERT: C 197 GLU cc_start: 0.6949 (tp30) cc_final: 0.6731 (tp30) REVERT: C 281 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8247 (mt) REVERT: D 313 MET cc_start: 0.7326 (tpt) cc_final: 0.7011 (tpt) REVERT: D 405 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7787 (ttp-110) REVERT: D 558 GLU cc_start: 0.7452 (tt0) cc_final: 0.7244 (tt0) REVERT: D 751 MET cc_start: 0.6312 (ptm) cc_final: 0.5841 (ptt) REVERT: D 791 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7403 (ttp) REVERT: D 839 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8310 (mtt90) REVERT: D 964 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6698 (tt0) outliers start: 63 outliers final: 18 residues processed: 554 average time/residue: 1.3709 time to fit residues: 846.8933 Evaluate side-chains 504 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 482 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 1292 GLU Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 791 MET Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1124 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 173 optimal weight: 0.3980 chunk 193 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 156 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 132 GLN A 983 ASN A1138 GLN B 207 ASN B 211 GLN B1283 GLN C 314 GLN C 660 ASN C 725 ASN D 163 GLN D 232 GLN ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 ASN D 781 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18651 Z= 0.153 Angle : 0.540 9.308 25429 Z= 0.278 Chirality : 0.038 0.161 2963 Planarity : 0.003 0.054 2951 Dihedral : 18.329 176.487 3085 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.36 % Allowed : 18.87 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.18), residues: 2054 helix: 2.44 (0.14), residues: 1261 sheet: 1.18 (0.39), residues: 181 loop : -0.59 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 589 HIS 0.003 0.000 HIS B 235 PHE 0.023 0.001 PHE B1388 TYR 0.024 0.001 TYR D 117 ARG 0.005 0.000 ARG D 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 484 time to evaluate : 2.071 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7338 (mtp180) REVERT: A 159 SER cc_start: 0.8318 (t) cc_final: 0.8073 (p) REVERT: A 189 GLU cc_start: 0.6642 (tp30) cc_final: 0.6430 (tp30) REVERT: A 228 GLU cc_start: 0.6443 (mp0) cc_final: 0.6018 (mp0) REVERT: A 1076 ILE cc_start: 0.8351 (tt) cc_final: 0.8108 (pt) REVERT: A 1156 PHE cc_start: 0.8009 (m-80) cc_final: 0.7682 (m-80) REVERT: B 234 VAL cc_start: 0.8585 (m) cc_final: 0.8343 (t) REVERT: B 272 ILE cc_start: 0.7984 (pt) cc_final: 0.7593 (mt) REVERT: B 1268 MET cc_start: 0.7575 (mmm) cc_final: 0.6655 (mpp) REVERT: B 1275 SER cc_start: 0.8096 (m) cc_final: 0.7867 (m) REVERT: B 1281 MET cc_start: 0.7782 (tpp) cc_final: 0.7445 (tpp) REVERT: B 1327 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7081 (mt-10) REVERT: C 197 GLU cc_start: 0.6959 (tp30) cc_final: 0.6759 (tp30) REVERT: C 281 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8143 (mt) REVERT: D 264 GLU cc_start: 0.5874 (mp0) cc_final: 0.5658 (mp0) REVERT: D 313 MET cc_start: 0.7340 (tpt) cc_final: 0.7040 (tpt) REVERT: D 658 LYS cc_start: 0.7961 (tppp) cc_final: 0.7612 (mmmm) REVERT: D 751 MET cc_start: 0.6416 (ptm) cc_final: 0.6022 (ptp) REVERT: D 785 ASP cc_start: 0.7341 (p0) cc_final: 0.7042 (p0) REVERT: D 804 SER cc_start: 0.8658 (p) cc_final: 0.8437 (m) REVERT: D 964 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6707 (tt0) outliers start: 64 outliers final: 20 residues processed: 506 average time/residue: 1.4652 time to fit residues: 822.8946 Evaluate side-chains 487 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 466 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 1012 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 GLN A1153 ASN B 211 GLN B1283 GLN B1393 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 610 GLN D 634 ASN ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 ASN D 852 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 18651 Z= 0.419 Angle : 0.686 13.810 25429 Z= 0.350 Chirality : 0.045 0.220 2963 Planarity : 0.004 0.058 2951 Dihedral : 18.542 172.149 3085 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.68 % Allowed : 19.61 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2054 helix: 2.01 (0.14), residues: 1261 sheet: 0.73 (0.38), residues: 183 loop : -0.75 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1033 HIS 0.007 0.002 HIS D1024 PHE 0.028 0.002 PHE D 431 TYR 0.024 0.002 TYR D 529 ARG 0.011 0.001 ARG D 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 530 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7339 (mtp180) REVERT: A 159 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 177 ARG cc_start: 0.7012 (tpp-160) cc_final: 0.6536 (tpt90) REVERT: A 189 GLU cc_start: 0.6934 (tp30) cc_final: 0.6700 (tp30) REVERT: A 210 LEU cc_start: 0.8128 (mt) cc_final: 0.7860 (mt) REVERT: A 228 GLU cc_start: 0.6789 (mp0) cc_final: 0.6456 (mp0) REVERT: A 1020 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7563 (mtpt) REVERT: B 209 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7787 (mtp) REVERT: B 234 VAL cc_start: 0.8734 (m) cc_final: 0.8453 (t) REVERT: B 1275 SER cc_start: 0.8093 (m) cc_final: 0.7864 (m) REVERT: B 1318 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7498 (mtp85) REVERT: B 1321 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8154 (p) REVERT: C 281 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8280 (mt) REVERT: D 78 SER cc_start: 0.7375 (m) cc_final: 0.7147 (p) REVERT: D 313 MET cc_start: 0.7297 (tpt) cc_final: 0.6915 (tpt) REVERT: D 405 ARG cc_start: 0.8131 (ttp-170) cc_final: 0.7921 (ttp-110) REVERT: D 544 ILE cc_start: 0.7714 (tt) cc_final: 0.7325 (tt) REVERT: D 561 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: D 644 LEU cc_start: 0.8294 (mm) cc_final: 0.8092 (mt) REVERT: D 658 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7701 (mmmm) REVERT: D 751 MET cc_start: 0.6875 (ptm) cc_final: 0.6575 (ptm) REVERT: D 791 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7361 (ttp) REVERT: D 926 LEU cc_start: 0.8341 (pp) cc_final: 0.8121 (pt) REVERT: D 941 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: D 964 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7098 (tt0) REVERT: D 1025 ASP cc_start: 0.7625 (m-30) cc_final: 0.7129 (m-30) outliers start: 89 outliers final: 33 residues processed: 562 average time/residue: 1.3879 time to fit residues: 868.9998 Evaluate side-chains 539 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 497 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 791 MET Chi-restraints excluded: chain D residue 941 GLU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1129 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 52 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 142 ASN A 221 GLN ** A1138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 GLN B1393 GLN C 653 ASN C 660 ASN D 178 ASN ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18651 Z= 0.186 Angle : 0.571 11.314 25429 Z= 0.294 Chirality : 0.039 0.173 2963 Planarity : 0.004 0.056 2951 Dihedral : 18.431 173.406 3085 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.26 % Allowed : 23.19 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.18), residues: 2054 helix: 2.33 (0.14), residues: 1247 sheet: 0.79 (0.39), residues: 181 loop : -0.69 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1033 HIS 0.003 0.001 HIS D 230 PHE 0.022 0.002 PHE D 431 TYR 0.020 0.001 TYR D 529 ARG 0.010 0.000 ARG A1157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 475 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7666 (mtp-110) cc_final: 0.7298 (mtp180) REVERT: A 159 SER cc_start: 0.8381 (t) cc_final: 0.8118 (p) REVERT: A 177 ARG cc_start: 0.6942 (tpp-160) cc_final: 0.6532 (tpt90) REVERT: A 228 GLU cc_start: 0.6711 (mp0) cc_final: 0.6485 (mp0) REVERT: B 234 VAL cc_start: 0.8658 (m) cc_final: 0.8426 (t) REVERT: B 276 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6874 (tm-30) REVERT: B 1281 MET cc_start: 0.7812 (tpp) cc_final: 0.7564 (tpp) REVERT: B 1287 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7265 (mtm) REVERT: B 1290 ASN cc_start: 0.7466 (m-40) cc_final: 0.7212 (m-40) REVERT: B 1321 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 1375 ASN cc_start: 0.7899 (p0) cc_final: 0.7460 (p0) REVERT: C 94 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8570 (t) REVERT: C 281 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8190 (mt) REVERT: C 637 THR cc_start: 0.8308 (p) cc_final: 0.7875 (m) REVERT: C 702 MET cc_start: 0.5657 (pmm) cc_final: 0.5130 (pmm) REVERT: C 740 LEU cc_start: 0.8413 (mt) cc_final: 0.8192 (mp) REVERT: D 113 GLU cc_start: 0.6523 (tp30) cc_final: 0.6305 (tp30) REVERT: D 195 LEU cc_start: 0.8308 (tt) cc_final: 0.8028 (tp) REVERT: D 313 MET cc_start: 0.7337 (tpt) cc_final: 0.6938 (tpt) REVERT: D 405 ARG cc_start: 0.8107 (ttp-170) cc_final: 0.7867 (ttp-110) REVERT: D 644 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7965 (mt) REVERT: D 658 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7711 (mmmm) REVERT: D 1025 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7089 (m-30) outliers start: 81 outliers final: 29 residues processed: 507 average time/residue: 1.5066 time to fit residues: 854.6053 Evaluate side-chains 500 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 464 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 351 HIS Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 821 THR Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 207 optimal weight: 40.0000 chunk 171 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 132 ASN B1393 GLN C 292 GLN D 610 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18651 Z= 0.246 Angle : 0.600 11.377 25429 Z= 0.307 Chirality : 0.040 0.172 2963 Planarity : 0.004 0.057 2951 Dihedral : 18.489 178.393 3085 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.84 % Allowed : 23.82 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2054 helix: 2.27 (0.14), residues: 1251 sheet: 0.77 (0.39), residues: 181 loop : -0.73 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 589 HIS 0.004 0.001 HIS D 586 PHE 0.021 0.002 PHE D 431 TYR 0.020 0.002 TYR D 529 ARG 0.009 0.000 ARG A1157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 491 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7665 (mtp-110) cc_final: 0.7211 (mtp180) REVERT: A 159 SER cc_start: 0.8346 (t) cc_final: 0.8026 (p) REVERT: A 177 ARG cc_start: 0.7012 (tpp-160) cc_final: 0.6650 (tpt90) REVERT: A 194 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6511 (tm-30) REVERT: B 234 VAL cc_start: 0.8722 (m) cc_final: 0.8488 (t) REVERT: B 276 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6881 (tm-30) REVERT: B 1281 MET cc_start: 0.7835 (tpp) cc_final: 0.7554 (tpp) REVERT: B 1287 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7249 (mtm) REVERT: B 1290 ASN cc_start: 0.7499 (m-40) cc_final: 0.7273 (m-40) REVERT: B 1318 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7400 (mtp85) REVERT: B 1375 ASN cc_start: 0.7870 (p0) cc_final: 0.7439 (p0) REVERT: C 281 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 637 THR cc_start: 0.8298 (p) cc_final: 0.7939 (m) REVERT: C 702 MET cc_start: 0.5774 (pmm) cc_final: 0.5404 (pmm) REVERT: D 113 GLU cc_start: 0.6549 (tp30) cc_final: 0.6233 (tp30) REVERT: D 313 MET cc_start: 0.7335 (tpt) cc_final: 0.6939 (tpt) REVERT: D 402 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7887 (mt) REVERT: D 405 ARG cc_start: 0.8080 (ttp-170) cc_final: 0.7806 (ttp-110) REVERT: D 561 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: D 644 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7994 (mt) REVERT: D 658 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7705 (mmmm) REVERT: D 791 MET cc_start: 0.7522 (ptm) cc_final: 0.7293 (ttp) REVERT: D 949 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6556 (ttt90) REVERT: D 1025 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7079 (m-30) outliers start: 92 outliers final: 47 residues processed: 524 average time/residue: 1.2791 time to fit residues: 747.7429 Evaluate side-chains 537 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 481 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1292 GLU Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain B residue 1370 LYS Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 351 HIS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 542 LYS Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 804 SER Chi-restraints excluded: chain D residue 949 ARG Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 206 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 106 GLN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 ASN B 132 ASN B1393 GLN ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18651 Z= 0.257 Angle : 0.615 14.133 25429 Z= 0.312 Chirality : 0.041 0.185 2963 Planarity : 0.004 0.057 2951 Dihedral : 18.442 175.289 3085 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.52 % Allowed : 24.87 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.18), residues: 2054 helix: 2.22 (0.14), residues: 1252 sheet: 0.66 (0.39), residues: 183 loop : -0.77 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 589 HIS 0.005 0.001 HIS D 230 PHE 0.023 0.002 PHE D 431 TYR 0.025 0.002 TYR D1086 ARG 0.008 0.001 ARG A1157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 497 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 SER cc_start: 0.8338 (t) cc_final: 0.8092 (p) REVERT: A 177 ARG cc_start: 0.7047 (tpp-160) cc_final: 0.6654 (tpt90) REVERT: B 234 VAL cc_start: 0.8697 (m) cc_final: 0.8477 (t) REVERT: B 276 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6872 (tm-30) REVERT: B 281 GLU cc_start: 0.7206 (tp30) cc_final: 0.6955 (tp30) REVERT: B 1287 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7204 (mtm) REVERT: B 1290 ASN cc_start: 0.7499 (m-40) cc_final: 0.7291 (t0) REVERT: B 1318 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7412 (mtp85) REVERT: B 1339 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8710 (mt) REVERT: B 1375 ASN cc_start: 0.7819 (p0) cc_final: 0.7409 (p0) REVERT: B 1392 GLN cc_start: 0.7731 (mt0) cc_final: 0.7436 (mt0) REVERT: C 281 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8291 (mt) REVERT: C 637 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7918 (t) REVERT: C 702 MET cc_start: 0.6026 (pmm) cc_final: 0.5782 (pmm) REVERT: D 313 MET cc_start: 0.7312 (tpt) cc_final: 0.6922 (tpt) REVERT: D 402 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7911 (mt) REVERT: D 561 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: D 644 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7987 (mt) REVERT: D 658 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7715 (mmmm) REVERT: D 791 MET cc_start: 0.7536 (ptm) cc_final: 0.7277 (ttp) REVERT: D 1025 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.6996 (m-30) outliers start: 86 outliers final: 46 residues processed: 528 average time/residue: 1.4373 time to fit residues: 843.4698 Evaluate side-chains 547 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 491 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1151 ASN Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1292 GLU Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1339 LEU Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 351 HIS Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 804 SER Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 132 GLN A 139 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 132 ASN B 211 GLN B1385 ASN B1393 GLN D 229 ASN ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18651 Z= 0.190 Angle : 0.598 12.569 25429 Z= 0.302 Chirality : 0.039 0.216 2963 Planarity : 0.003 0.057 2951 Dihedral : 18.323 171.432 3085 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.15 % Allowed : 25.55 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 2054 helix: 2.34 (0.15), residues: 1250 sheet: 0.73 (0.40), residues: 179 loop : -0.78 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1033 HIS 0.003 0.001 HIS D 230 PHE 0.020 0.002 PHE D 431 TYR 0.025 0.002 TYR D1086 ARG 0.014 0.001 ARG D 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 492 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 SER cc_start: 0.8301 (t) cc_final: 0.7988 (p) REVERT: B 234 VAL cc_start: 0.8669 (m) cc_final: 0.8461 (t) REVERT: B 281 GLU cc_start: 0.7171 (tp30) cc_final: 0.6897 (tp30) REVERT: B 1281 MET cc_start: 0.7866 (tpp) cc_final: 0.7542 (tpp) REVERT: B 1287 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7225 (mtm) REVERT: B 1290 ASN cc_start: 0.7479 (m-40) cc_final: 0.7272 (m-40) REVERT: B 1318 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7281 (mtp85) REVERT: B 1327 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7089 (mt-10) REVERT: B 1339 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 1370 LYS cc_start: 0.8507 (tptm) cc_final: 0.8282 (tttm) REVERT: B 1375 ASN cc_start: 0.7786 (p0) cc_final: 0.7414 (p0) REVERT: B 1392 GLN cc_start: 0.7708 (mt0) cc_final: 0.7463 (mt0) REVERT: B 1410 LYS cc_start: 0.7421 (mtmm) cc_final: 0.7206 (mtpt) REVERT: C 281 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8265 (mt) REVERT: C 637 THR cc_start: 0.8283 (p) cc_final: 0.7921 (m) REVERT: D 165 GLU cc_start: 0.6477 (tm-30) cc_final: 0.6065 (tm-30) REVERT: D 195 LEU cc_start: 0.8176 (tt) cc_final: 0.7912 (tp) REVERT: D 313 MET cc_start: 0.7308 (tpt) cc_final: 0.6902 (tpt) REVERT: D 398 LYS cc_start: 0.7288 (tppp) cc_final: 0.7035 (mmmm) REVERT: D 561 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: D 644 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7919 (mt) REVERT: D 658 LYS cc_start: 0.7949 (tppp) cc_final: 0.7714 (mmmm) REVERT: D 791 MET cc_start: 0.7504 (ptm) cc_final: 0.7211 (ttp) REVERT: D 1025 ASP cc_start: 0.7500 (m-30) cc_final: 0.7194 (m-30) REVERT: D 1109 LYS cc_start: 0.7318 (pttt) cc_final: 0.7115 (ptmm) outliers start: 79 outliers final: 44 residues processed: 526 average time/residue: 1.4414 time to fit residues: 842.5076 Evaluate side-chains 531 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 481 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1151 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1339 LEU Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 351 HIS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 804 SER Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 0.0870 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B1385 ASN B1393 GLN D 162 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18651 Z= 0.247 Angle : 0.634 13.080 25429 Z= 0.322 Chirality : 0.041 0.234 2963 Planarity : 0.004 0.058 2951 Dihedral : 18.306 171.222 3085 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.10 % Allowed : 26.55 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 2054 helix: 2.22 (0.15), residues: 1257 sheet: 0.67 (0.39), residues: 182 loop : -0.74 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 589 HIS 0.004 0.001 HIS D 230 PHE 0.022 0.002 PHE D 431 TYR 0.026 0.002 TYR D 117 ARG 0.010 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 488 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 SER cc_start: 0.8307 (t) cc_final: 0.8004 (p) REVERT: B 1287 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7242 (mtm) REVERT: B 1290 ASN cc_start: 0.7516 (m-40) cc_final: 0.7304 (t0) REVERT: B 1318 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7369 (mtp85) REVERT: B 1327 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7084 (mm-30) REVERT: B 1375 ASN cc_start: 0.7776 (p0) cc_final: 0.7411 (p0) REVERT: B 1392 GLN cc_start: 0.7719 (mt0) cc_final: 0.7478 (mt0) REVERT: B 1410 LYS cc_start: 0.7436 (mtmm) cc_final: 0.7223 (mtpt) REVERT: C 281 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8294 (mt) REVERT: C 637 THR cc_start: 0.8248 (p) cc_final: 0.7907 (m) REVERT: D 165 GLU cc_start: 0.6568 (tm-30) cc_final: 0.6169 (tm-30) REVERT: D 195 LEU cc_start: 0.8226 (tt) cc_final: 0.7926 (tp) REVERT: D 313 MET cc_start: 0.7296 (tpt) cc_final: 0.6909 (tpt) REVERT: D 351 HIS cc_start: 0.6693 (OUTLIER) cc_final: 0.6387 (t-170) REVERT: D 398 LYS cc_start: 0.7343 (tppp) cc_final: 0.7117 (mmmm) REVERT: D 561 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: D 610 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: D 644 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7974 (mt) REVERT: D 658 LYS cc_start: 0.7947 (tppp) cc_final: 0.7697 (mmmm) REVERT: D 791 MET cc_start: 0.7530 (ptm) cc_final: 0.7261 (ttp) REVERT: D 1025 ASP cc_start: 0.7522 (m-30) cc_final: 0.7007 (m-30) REVERT: D 1109 LYS cc_start: 0.7354 (pttt) cc_final: 0.7130 (ptmm) outliers start: 78 outliers final: 49 residues processed: 518 average time/residue: 1.4596 time to fit residues: 839.0021 Evaluate side-chains 542 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 486 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1027 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1151 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1330 LEU Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 351 HIS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 610 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 804 SER Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 213 optimal weight: 10.0000 chunk 196 optimal weight: 0.0050 chunk 169 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 0.2980 chunk 134 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 GLN B 132 ASN B 211 GLN B1385 ASN B1393 GLN D 229 ASN D 237 GLN ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18651 Z= 0.171 Angle : 0.618 13.260 25429 Z= 0.311 Chirality : 0.039 0.263 2963 Planarity : 0.004 0.057 2951 Dihedral : 18.189 171.307 3085 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.05 % Allowed : 28.18 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2054 helix: 2.36 (0.15), residues: 1246 sheet: 0.75 (0.39), residues: 177 loop : -0.69 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 589 HIS 0.003 0.000 HIS D1024 PHE 0.018 0.001 PHE D 431 TYR 0.029 0.001 TYR D 117 ARG 0.012 0.001 ARG D1021 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 487 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8448 (mmt) cc_final: 0.8237 (mmp) REVERT: A 159 SER cc_start: 0.8274 (t) cc_final: 0.8041 (p) REVERT: B 1290 ASN cc_start: 0.7460 (m-40) cc_final: 0.7242 (m-40) REVERT: B 1318 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7208 (mtp85) REVERT: B 1327 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7309 (mt-10) REVERT: B 1352 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6723 (mt-10) REVERT: B 1375 ASN cc_start: 0.7746 (p0) cc_final: 0.7382 (p0) REVERT: B 1392 GLN cc_start: 0.7705 (mt0) cc_final: 0.7393 (mt0) REVERT: C 281 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8213 (mt) REVERT: C 637 THR cc_start: 0.8237 (p) cc_final: 0.7932 (m) REVERT: D 165 GLU cc_start: 0.6483 (tm-30) cc_final: 0.6130 (tm-30) REVERT: D 166 ASN cc_start: 0.7137 (t0) cc_final: 0.6709 (t0) REVERT: D 313 MET cc_start: 0.7287 (tpt) cc_final: 0.6928 (tpt) REVERT: D 398 LYS cc_start: 0.7352 (tppp) cc_final: 0.7084 (mmmm) REVERT: D 561 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: D 644 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7864 (mt) REVERT: D 658 LYS cc_start: 0.7907 (tppp) cc_final: 0.7657 (mmmm) REVERT: D 791 MET cc_start: 0.7487 (ptm) cc_final: 0.7172 (ttp) REVERT: D 1025 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7103 (m-30) outliers start: 58 outliers final: 34 residues processed: 510 average time/residue: 1.4264 time to fit residues: 807.8099 Evaluate side-chains 518 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 479 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 804 SER Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 156 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 139 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 GLN A1153 ASN B 132 ASN B 211 GLN B1385 ASN B1393 GLN D 249 HIS ** D 715 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.151795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123021 restraints weight = 24743.985| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.72 r_work: 0.3345 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18651 Z= 0.232 Angle : 0.639 11.693 25429 Z= 0.320 Chirality : 0.040 0.251 2963 Planarity : 0.004 0.058 2951 Dihedral : 18.197 171.217 3085 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.79 % Allowed : 28.29 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 2054 helix: 2.26 (0.15), residues: 1258 sheet: 0.75 (0.40), residues: 178 loop : -0.75 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 589 HIS 0.004 0.001 HIS D 230 PHE 0.020 0.002 PHE A1103 TYR 0.025 0.002 TYR D 117 ARG 0.013 0.001 ARG D1021 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10648.24 seconds wall clock time: 189 minutes 37.66 seconds (11377.66 seconds total)