Starting phenix.real_space_refine on Fri Feb 16 02:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/02_2024/6mcc_9067_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/02_2024/6mcc_9067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/02_2024/6mcc_9067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/02_2024/6mcc_9067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/02_2024/6mcc_9067_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcc_9067/02_2024/6mcc_9067_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 26 5.16 5 C 8551 2.51 5 N 2458 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 919": "NH1" <-> "NH2" Residue "A PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1333": "NH1" <-> "NH2" Residue "A ARG 1335": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14175 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2494 Unusual residues: {'GTP': 1} Classifications: {'RNA': 115, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 18, 'rna3p': 96, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "A" Number of atoms: 10715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10715 Classifications: {'peptide': 1364} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 35, 'TRANS': 1328} Unresolved non-hydrogen bonds: 441 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 389 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 226 Chain: "C" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 966 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLU:plan': 17, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 8.59, per 1000 atoms: 0.61 Number of scatterers: 14175 At special positions: 0 Unit cell: (92, 121.9, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 118 15.00 O 3022 8.00 N 2458 7.00 C 8551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 2.4 seconds 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 7 sheets defined 39.4% alpha, 6.8% beta 27 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 8.08 Creating SS restraints... Processing helix chain 'A' and resid 61 through 85 Processing helix chain 'A' and resid 90 through 93 No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.583A pdb=" N HIS A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 218 through 228 removed outlier: 5.250A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.806A pdb=" N ASN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 305 removed outlier: 5.711A pdb=" N ASP A 288 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 339 removed outlier: 3.553A pdb=" N ILE A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.689A pdb=" N ILE A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 363' Processing helix chain 'A' and resid 369 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 390 through 393 No H-bonds generated for 'chain 'A' and resid 390 through 393' Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 432 through 435 removed outlier: 3.771A pdb=" N ASP A 435 " --> pdb=" O PHE A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.670A pdb=" N GLU A 493 " --> pdb=" O GLN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 605 through 608 No H-bonds generated for 'chain 'A' and resid 605 through 608' Processing helix chain 'A' and resid 613 through 625 Processing helix chain 'A' and resid 631 through 639 removed outlier: 4.182A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 651 No H-bonds generated for 'chain 'A' and resid 648 through 651' Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'A' and resid 703 through 711 removed outlier: 4.003A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 removed outlier: 4.293A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 750 removed outlier: 4.280A pdb=" N LYS A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 775 through 778 No H-bonds generated for 'chain 'A' and resid 775 through 778' Processing helix chain 'A' and resid 781 through 790 removed outlier: 3.844A pdb=" N ILE A 788 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 809 through 817 removed outlier: 3.570A pdb=" N GLN A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 880 through 888 removed outlier: 3.727A pdb=" N ARG A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 885 " --> pdb=" O ASN A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 903 removed outlier: 3.908A pdb=" N LYS A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ALA A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 919 Processing helix chain 'A' and resid 926 through 939 removed outlier: 3.989A pdb=" N MET A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 968 Processing helix chain 'A' and resid 981 through 998 removed outlier: 3.894A pdb=" N ASP A 986 " --> pdb=" O HIS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1042 through 1045 Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1080 through 1087 Processing helix chain 'A' and resid 1171 through 1176 Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1192 through 1194 No H-bonds generated for 'chain 'A' and resid 1192 through 1194' Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1230 through 1239 Processing helix chain 'A' and resid 1249 through 1261 Processing helix chain 'A' and resid 1263 through 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1269 through 1280 Processing helix chain 'A' and resid 1284 through 1297 removed outlier: 3.570A pdb=" N HIS A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1315 removed outlier: 4.506A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.872A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 31 through 34 No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 109 through 120 Processing sheet with id= A, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.191A pdb=" N ASN A1093 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 52 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A1095 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 29 through 33 Processing sheet with id= C, first strand: chain 'A' and resid 837 through 840 Processing sheet with id= D, first strand: chain 'A' and resid 1196 through 1199 removed outlier: 7.265A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1210 through 1214 removed outlier: 3.971A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 126 through 128 removed outlier: 3.741A pdb=" N LYS C 127 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR C 39 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 78 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 69 through 72 removed outlier: 3.602A pdb=" N LEU C 71 " --> pdb=" O PHE C 88 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE C 88 " --> pdb=" O LEU C 71 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 6.31 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2348 1.32 - 1.44: 4340 1.44 - 1.57: 7714 1.57 - 1.69: 232 1.69 - 1.81: 48 Bond restraints: 14682 Sorted by residual: bond pdb=" C6 GTP B 1 " pdb=" O6 GTP B 1 " ideal model delta sigma weight residual 1.230 1.387 -0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C5 GTP B 1 " pdb=" C6 GTP B 1 " ideal model delta sigma weight residual 1.390 1.458 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O3B GTP B 1 " pdb=" PB GTP B 1 " ideal model delta sigma weight residual 1.610 1.550 0.060 2.00e-02 2.50e+03 9.00e+00 bond pdb=" C2 GTP B 1 " pdb=" N1 GTP B 1 " ideal model delta sigma weight residual 1.380 1.438 -0.058 2.00e-02 2.50e+03 8.37e+00 ... (remaining 14677 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.61: 615 104.61 - 112.01: 7052 112.01 - 119.40: 5456 119.40 - 126.80: 6880 126.80 - 134.19: 432 Bond angle restraints: 20435 Sorted by residual: angle pdb=" C ASP A 353 " pdb=" N GLN A 354 " pdb=" CA GLN A 354 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C ASP C 101 " pdb=" N GLU C 102 " pdb=" CA GLU C 102 " ideal model delta sigma weight residual 121.54 131.54 -10.00 1.91e+00 2.74e-01 2.74e+01 angle pdb=" CA THR C 107 " pdb=" CB THR C 107 " pdb=" CG2 THR C 107 " ideal model delta sigma weight residual 110.50 118.04 -7.54 1.70e+00 3.46e-01 1.97e+01 angle pdb=" N GLY A1133 " pdb=" CA GLY A1133 " pdb=" C GLY A1133 " ideal model delta sigma weight residual 110.20 115.93 -5.73 1.32e+00 5.74e-01 1.89e+01 angle pdb=" C3' A B 86 " pdb=" O3' A B 86 " pdb=" P A B 87 " ideal model delta sigma weight residual 120.20 126.65 -6.45 1.50e+00 4.44e-01 1.85e+01 ... (remaining 20430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8552 35.47 - 70.95: 366 70.95 - 106.42: 39 106.42 - 141.90: 1 141.90 - 177.37: 4 Dihedral angle restraints: 8962 sinusoidal: 4561 harmonic: 4401 Sorted by residual: dihedral pdb=" O4' C B 88 " pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sinusoidal sigma weight residual 200.00 40.60 159.40 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U B 7 " pdb=" C1' U B 7 " pdb=" N1 U B 7 " pdb=" C2 U B 7 " ideal model delta sinusoidal sigma weight residual 232.00 56.24 175.76 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA THR C 107 " pdb=" C THR C 107 " pdb=" N GLU C 108 " pdb=" CA GLU C 108 " ideal model delta harmonic sigma weight residual -180.00 -145.35 -34.65 0 5.00e+00 4.00e-02 4.80e+01 ... (remaining 8959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.963: 2409 0.963 - 1.925: 0 1.925 - 2.888: 0 2.888 - 3.851: 0 3.851 - 4.814: 2 Chirality restraints: 2411 Sorted by residual: chirality pdb=" C2' GTP B 1 " pdb=" C1' GTP B 1 " pdb=" C3' GTP B 1 " pdb=" O2' GTP B 1 " both_signs ideal model delta sigma weight residual False -2.47 2.34 -4.81 2.00e-01 2.50e+01 5.79e+02 chirality pdb=" C4' GTP B 1 " pdb=" C3' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O4' GTP B 1 " both_signs ideal model delta sigma weight residual False -2.47 2.25 -4.72 2.00e-01 2.50e+01 5.58e+02 chirality pdb=" C1' A B 8 " pdb=" O4' A B 8 " pdb=" C2' A B 8 " pdb=" N9 A B 8 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 2408 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 8 " -0.035 2.00e-02 2.50e+03 1.80e-02 8.94e+00 pdb=" N9 A B 8 " 0.047 2.00e-02 2.50e+03 pdb=" C8 A B 8 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 8 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 8 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B 8 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A B 8 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B 8 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 8 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 8 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 302 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C LEU A 302 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A 302 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 303 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 295 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C ASN A 295 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 295 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 296 " 0.015 2.00e-02 2.50e+03 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4123 2.81 - 3.33: 12952 3.33 - 3.86: 24637 3.86 - 4.38: 26604 4.38 - 4.90: 42182 Nonbonded interactions: 110498 Sorted by model distance: nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.290 2.440 nonbonded pdb=" O2' U B 62 " pdb=" OE1 GLN A 402 " model vdw 2.314 2.440 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.317 2.440 nonbonded pdb=" O TYR A 136 " pdb=" OG SER A 318 " model vdw 2.319 2.440 nonbonded pdb=" O ARG A 925 " pdb=" OG1 THR A 928 " model vdw 2.328 2.440 ... (remaining 110493 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 group one per residue 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.400 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 47.940 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.006 0.157 14682 Z= 0.395 Angle : 1.038 12.694 20435 Z= 0.537 Chirality : 0.148 4.814 2411 Planarity : 0.006 0.052 2194 Dihedral : 17.836 177.369 6114 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 1.08 % Allowed : 9.35 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.17), residues: 1490 helix: -3.23 (0.14), residues: 609 sheet: -1.76 (0.45), residues: 111 loop : -3.02 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 476 HIS 0.009 0.002 HIS A 160 PHE 0.044 0.003 PHE A1008 TYR 0.023 0.003 TYR A 72 ARG 0.022 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 240 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8879 (p-90) cc_final: 0.8612 (p-90) REVERT: A 241 LEU cc_start: 0.9103 (mm) cc_final: 0.8611 (pp) REVERT: A 586 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8452 (mtm-85) REVERT: A 879 MET cc_start: 0.7602 (mtt) cc_final: 0.7231 (mtt) REVERT: A 883 TRP cc_start: 0.6278 (m-10) cc_final: 0.5804 (m-10) REVERT: A 1205 GLU cc_start: 0.8032 (tt0) cc_final: 0.7777 (tt0) REVERT: C 75 PHE cc_start: 0.8124 (p90) cc_final: 0.7699 (p90) outliers start: 13 outliers final: 3 residues processed: 249 average time/residue: 0.2844 time to fit residues: 103.1609 Evaluate side-chains 147 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 662 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 412 HIS A 489 GLN A 522 ASN A 674 GLN ** A 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN A 930 HIS A 980 ASN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 ASN A1093 ASN A1101 GLN A1297 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14682 Z= 0.175 Angle : 0.650 13.134 20435 Z= 0.321 Chirality : 0.039 0.202 2411 Planarity : 0.004 0.041 2194 Dihedral : 19.700 176.377 3378 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.56 % Allowed : 13.40 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.19), residues: 1490 helix: -1.77 (0.18), residues: 619 sheet: -1.30 (0.49), residues: 100 loop : -2.69 (0.19), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.032 0.002 PHE A1008 TYR 0.013 0.001 TYR A 812 ARG 0.005 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 179 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8482 (mp) REVERT: A 18 TRP cc_start: 0.8793 (p-90) cc_final: 0.8148 (p-90) REVERT: A 304 ASP cc_start: 0.8889 (t70) cc_final: 0.8587 (t70) REVERT: A 706 GLU cc_start: 0.7718 (mp0) cc_final: 0.7277 (mp0) REVERT: A 879 MET cc_start: 0.7765 (mtt) cc_final: 0.7447 (mtt) REVERT: A 883 TRP cc_start: 0.5809 (m-10) cc_final: 0.5393 (m-90) REVERT: A 1046 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: A 1074 TRP cc_start: 0.5310 (t60) cc_final: 0.4926 (t60) REVERT: A 1205 GLU cc_start: 0.7921 (tt0) cc_final: 0.7639 (tt0) REVERT: A 1365 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8393 (tt) REVERT: C 97 ASP cc_start: 0.7815 (t0) cc_final: 0.6962 (p0) REVERT: C 120 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8714 (tp) outliers start: 43 outliers final: 18 residues processed: 212 average time/residue: 0.2325 time to fit residues: 74.9288 Evaluate side-chains 159 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 129 optimal weight: 0.3980 chunk 144 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 116 optimal weight: 0.0050 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 739 GLN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14682 Z= 0.155 Angle : 0.605 11.750 20435 Z= 0.296 Chirality : 0.038 0.195 2411 Planarity : 0.003 0.034 2194 Dihedral : 19.483 177.681 3378 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.89 % Allowed : 16.21 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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 (0.20), residues: 1490 helix: -0.98 (0.20), residues: 617 sheet: -1.08 (0.50), residues: 100 loop : -2.46 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 476 HIS 0.004 0.001 HIS A 328 PHE 0.029 0.001 PHE A1008 TYR 0.021 0.001 TYR A1356 ARG 0.005 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 172 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8755 (p-90) cc_final: 0.8094 (p-90) REVERT: A 152 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8500 (ptt90) REVERT: A 279 LEU cc_start: 0.9275 (mm) cc_final: 0.9020 (mm) REVERT: A 422 ILE cc_start: 0.9492 (tp) cc_final: 0.9151 (tp) REVERT: A 706 GLU cc_start: 0.7821 (mp0) cc_final: 0.7336 (mp0) REVERT: A 708 ILE cc_start: 0.8860 (mt) cc_final: 0.8547 (mt) REVERT: A 712 GLN cc_start: 0.8200 (mm110) cc_final: 0.7576 (mm110) REVERT: A 759 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8740 (pp) REVERT: A 786 GLU cc_start: 0.8824 (pm20) cc_final: 0.8402 (tt0) REVERT: A 879 MET cc_start: 0.7908 (mtt) cc_final: 0.7527 (mtt) REVERT: A 883 TRP cc_start: 0.5804 (m-10) cc_final: 0.5259 (m-90) REVERT: A 1021 MET cc_start: 0.7887 (tpp) cc_final: 0.7547 (tpp) REVERT: A 1046 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: A 1118 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7977 (tttt) REVERT: A 1164 LEU cc_start: 0.9428 (tp) cc_final: 0.9214 (tt) REVERT: A 1365 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8409 (tt) REVERT: C 97 ASP cc_start: 0.7898 (t0) cc_final: 0.7176 (p0) REVERT: C 100 GLU cc_start: 0.8530 (mp0) cc_final: 0.8309 (mp0) REVERT: C 120 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8741 (tp) outliers start: 47 outliers final: 23 residues processed: 206 average time/residue: 0.2305 time to fit residues: 74.9018 Evaluate side-chains 169 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 0.3980 chunk 97 optimal weight: 20.0000 chunk 146 optimal weight: 0.0870 chunk 154 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14682 Z= 0.265 Angle : 0.651 10.561 20435 Z= 0.323 Chirality : 0.041 0.193 2411 Planarity : 0.004 0.036 2194 Dihedral : 19.496 175.997 3378 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.71 % Allowed : 17.29 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.31 (0.21), residues: 1490 helix: -0.76 (0.20), residues: 617 sheet: -1.08 (0.51), residues: 100 loop : -2.30 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A1074 HIS 0.006 0.001 HIS A 160 PHE 0.027 0.002 PHE A1008 TYR 0.025 0.002 TYR A 568 ARG 0.004 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 152 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8801 (p-90) cc_final: 0.7965 (p-90) REVERT: A 152 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8566 (ptt90) REVERT: A 279 LEU cc_start: 0.9264 (mm) cc_final: 0.8954 (mm) REVERT: A 706 GLU cc_start: 0.7922 (mp0) cc_final: 0.7537 (mp0) REVERT: A 759 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8685 (pp) REVERT: A 786 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: A 817 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.6076 (tt0) REVERT: A 879 MET cc_start: 0.7702 (mtt) cc_final: 0.7179 (mtt) REVERT: A 920 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 1046 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: A 1118 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7997 (tttt) REVERT: A 1164 LEU cc_start: 0.9514 (tp) cc_final: 0.9287 (tt) REVERT: A 1296 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8803 (tmmm) REVERT: A 1313 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7106 (m-10) REVERT: A 1365 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8599 (tm) REVERT: C 97 ASP cc_start: 0.8174 (t0) cc_final: 0.7524 (t0) REVERT: C 120 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8939 (tp) outliers start: 57 outliers final: 33 residues processed: 195 average time/residue: 0.2232 time to fit residues: 68.5404 Evaluate side-chains 183 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 140 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1296 LYS Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 0.2980 chunk 63 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14682 Z= 0.199 Angle : 0.616 10.123 20435 Z= 0.301 Chirality : 0.039 0.180 2411 Planarity : 0.003 0.034 2194 Dihedral : 19.423 174.283 3378 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.47 % Allowed : 18.44 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.02 (0.21), residues: 1490 helix: -0.48 (0.21), residues: 616 sheet: -0.94 (0.51), residues: 100 loop : -2.16 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A1074 HIS 0.005 0.001 HIS A 328 PHE 0.026 0.001 PHE A1008 TYR 0.018 0.001 TYR A 568 ARG 0.003 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 153 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8757 (p-90) cc_final: 0.7872 (p-90) REVERT: A 152 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8522 (ptt90) REVERT: A 279 LEU cc_start: 0.9267 (mm) cc_final: 0.8961 (mm) REVERT: A 751 MET cc_start: 0.7986 (ttt) cc_final: 0.7781 (ptm) REVERT: A 759 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8700 (pp) REVERT: A 762 GLU cc_start: 0.7548 (pm20) cc_final: 0.7309 (pm20) REVERT: A 879 MET cc_start: 0.7831 (mtt) cc_final: 0.7313 (mtt) REVERT: A 920 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8030 (tm-30) REVERT: A 977 GLU cc_start: 0.8785 (mp0) cc_final: 0.8490 (mp0) REVERT: A 1021 MET cc_start: 0.7774 (tpp) cc_final: 0.7084 (tpp) REVERT: A 1164 LEU cc_start: 0.9496 (tp) cc_final: 0.9281 (tt) REVERT: A 1296 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8828 (tmmm) REVERT: A 1365 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8578 (tm) REVERT: C 97 ASP cc_start: 0.8209 (t0) cc_final: 0.7447 (t0) REVERT: C 120 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8944 (tp) outliers start: 54 outliers final: 35 residues processed: 194 average time/residue: 0.2327 time to fit residues: 70.8663 Evaluate side-chains 177 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 137 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1296 LYS Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.2980 chunk 38 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14682 Z= 0.172 Angle : 0.598 9.667 20435 Z= 0.290 Chirality : 0.038 0.171 2411 Planarity : 0.003 0.034 2194 Dihedral : 19.325 175.036 3378 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.97 % Allowed : 19.52 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.75 (0.21), residues: 1490 helix: -0.26 (0.21), residues: 616 sheet: -0.73 (0.52), residues: 100 loop : -2.01 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1074 HIS 0.006 0.001 HIS A 328 PHE 0.025 0.001 PHE A1008 TYR 0.015 0.001 TYR A 639 ARG 0.004 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8730 (p-90) cc_final: 0.7772 (p-90) REVERT: A 152 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8500 (ptt90) REVERT: A 279 LEU cc_start: 0.9255 (mm) cc_final: 0.9004 (mm) REVERT: A 383 MET cc_start: 0.8782 (mmp) cc_final: 0.8014 (mmt) REVERT: A 759 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8701 (pp) REVERT: A 761 ILE cc_start: 0.8842 (pp) cc_final: 0.8561 (pp) REVERT: A 762 GLU cc_start: 0.7398 (pm20) cc_final: 0.7196 (pm20) REVERT: A 879 MET cc_start: 0.7833 (mtt) cc_final: 0.7271 (mtt) REVERT: A 977 GLU cc_start: 0.8746 (mp0) cc_final: 0.8470 (mp0) REVERT: A 1021 MET cc_start: 0.7783 (tpp) cc_final: 0.7389 (tpp) REVERT: A 1164 LEU cc_start: 0.9499 (tp) cc_final: 0.9278 (tt) REVERT: A 1365 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8608 (tm) REVERT: C 97 ASP cc_start: 0.8239 (t0) cc_final: 0.7479 (t0) REVERT: C 120 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8922 (tp) outliers start: 48 outliers final: 34 residues processed: 197 average time/residue: 0.2398 time to fit residues: 72.0150 Evaluate side-chains 175 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 40.0000 chunk 87 optimal weight: 0.0570 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14682 Z= 0.346 Angle : 0.699 11.222 20435 Z= 0.352 Chirality : 0.043 0.179 2411 Planarity : 0.004 0.039 2194 Dihedral : 19.452 174.426 3378 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.80 % Allowed : 20.26 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.01 (0.21), residues: 1490 helix: -0.57 (0.20), residues: 629 sheet: -0.78 (0.53), residues: 102 loop : -2.11 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A1074 HIS 0.007 0.001 HIS A 160 PHE 0.023 0.002 PHE A1008 TYR 0.020 0.002 TYR A 136 ARG 0.005 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 144 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8914 (p-90) cc_final: 0.8121 (p-90) REVERT: A 84 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7719 (tp30) REVERT: A 152 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8526 (ptt90) REVERT: A 279 LEU cc_start: 0.9253 (mm) cc_final: 0.8994 (mm) REVERT: A 383 MET cc_start: 0.8742 (mmp) cc_final: 0.8057 (mmt) REVERT: A 586 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7493 (ttt180) REVERT: A 759 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8758 (pp) REVERT: A 761 ILE cc_start: 0.8849 (pp) cc_final: 0.8464 (pp) REVERT: A 879 MET cc_start: 0.7762 (mtt) cc_final: 0.7274 (mtt) REVERT: A 898 ASP cc_start: 0.8766 (m-30) cc_final: 0.7806 (t0) REVERT: A 1021 MET cc_start: 0.7721 (tpp) cc_final: 0.7354 (tpp) REVERT: A 1043 MET cc_start: 0.8761 (tpp) cc_final: 0.8393 (tpp) REVERT: A 1044 ASN cc_start: 0.8339 (m110) cc_final: 0.8130 (m110) REVERT: A 1164 LEU cc_start: 0.9535 (tp) cc_final: 0.9329 (tt) REVERT: A 1313 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7317 (m-10) REVERT: A 1365 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8675 (tm) REVERT: C 91 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7106 (tm-30) REVERT: C 97 ASP cc_start: 0.8397 (t0) cc_final: 0.7639 (t0) REVERT: C 120 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8974 (tp) outliers start: 58 outliers final: 40 residues processed: 190 average time/residue: 0.2270 time to fit residues: 67.9528 Evaluate side-chains 184 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 139 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 98 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14682 Z= 0.148 Angle : 0.617 15.448 20435 Z= 0.295 Chirality : 0.038 0.354 2411 Planarity : 0.003 0.036 2194 Dihedral : 19.271 176.032 3378 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.23 % Allowed : 21.84 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.55 (0.21), residues: 1490 helix: -0.08 (0.22), residues: 596 sheet: -0.73 (0.52), residues: 100 loop : -1.86 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1074 HIS 0.006 0.001 HIS A 328 PHE 0.030 0.001 PHE A1008 TYR 0.016 0.001 TYR A 639 ARG 0.005 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8760 (p-90) cc_final: 0.7944 (p-90) REVERT: A 47 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7761 (tt) REVERT: A 152 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8113 (ptt90) REVERT: A 321 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7583 (ppp) REVERT: A 383 MET cc_start: 0.8755 (mmp) cc_final: 0.8041 (mmt) REVERT: A 618 ASP cc_start: 0.8865 (p0) cc_final: 0.8567 (p0) REVERT: A 759 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8473 (pp) REVERT: A 781 MET cc_start: 0.8442 (tmm) cc_final: 0.7810 (ppp) REVERT: A 879 MET cc_start: 0.8004 (mtt) cc_final: 0.7531 (mtt) REVERT: A 1000 LYS cc_start: 0.8462 (tmtt) cc_final: 0.8164 (tptt) REVERT: A 1164 LEU cc_start: 0.9485 (tp) cc_final: 0.9270 (tt) REVERT: C 35 ASN cc_start: 0.9022 (m110) cc_final: 0.8658 (m110) REVERT: C 91 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7151 (tm-30) REVERT: C 97 ASP cc_start: 0.8303 (t0) cc_final: 0.7612 (t0) outliers start: 39 outliers final: 22 residues processed: 195 average time/residue: 0.2328 time to fit residues: 71.1298 Evaluate side-chains 174 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 95 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14682 Z= 0.324 Angle : 0.718 15.076 20435 Z= 0.356 Chirality : 0.044 0.328 2411 Planarity : 0.004 0.038 2194 Dihedral : 19.357 174.754 3378 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.06 % Allowed : 23.49 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.88 (0.21), residues: 1490 helix: -0.46 (0.21), residues: 625 sheet: -0.66 (0.55), residues: 100 loop : -2.03 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A1074 HIS 0.006 0.001 HIS A 160 PHE 0.025 0.002 PHE A 446 TYR 0.013 0.002 TYR A 812 ARG 0.005 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8924 (p-90) cc_final: 0.8198 (p-90) REVERT: A 152 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8227 (ptt90) REVERT: A 406 ASP cc_start: 0.8405 (m-30) cc_final: 0.8108 (m-30) REVERT: A 586 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7422 (ttt180) REVERT: A 738 LEU cc_start: 0.8371 (tt) cc_final: 0.7412 (mt) REVERT: A 759 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8533 (pp) REVERT: A 781 MET cc_start: 0.8514 (tmm) cc_final: 0.7973 (ppp) REVERT: A 879 MET cc_start: 0.7772 (mtt) cc_final: 0.7298 (mtt) REVERT: A 898 ASP cc_start: 0.8771 (m-30) cc_final: 0.7809 (t0) REVERT: A 1000 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8191 (tptt) REVERT: A 1021 MET cc_start: 0.7763 (tpp) cc_final: 0.7260 (tpp) REVERT: A 1043 MET cc_start: 0.8704 (tpp) cc_final: 0.8309 (tpp) REVERT: A 1164 LEU cc_start: 0.9534 (tp) cc_final: 0.9333 (tt) REVERT: C 91 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7082 (tm-30) REVERT: C 97 ASP cc_start: 0.8452 (t0) cc_final: 0.7838 (t0) outliers start: 37 outliers final: 27 residues processed: 176 average time/residue: 0.2287 time to fit residues: 62.6052 Evaluate side-chains 173 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14682 Z= 0.160 Angle : 0.646 15.904 20435 Z= 0.309 Chirality : 0.039 0.292 2411 Planarity : 0.003 0.040 2194 Dihedral : 19.166 176.521 3378 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.23 % Allowed : 23.99 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.52 (0.22), residues: 1490 helix: -0.12 (0.22), residues: 607 sheet: -0.58 (0.54), residues: 100 loop : -1.82 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1074 HIS 0.005 0.001 HIS A 328 PHE 0.022 0.001 PHE A 446 TYR 0.015 0.001 TYR A 155 ARG 0.003 0.000 ARG A1212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8144 (ptt90) REVERT: A 321 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7511 (ppp) REVERT: A 383 MET cc_start: 0.8771 (mmp) cc_final: 0.8022 (mmt) REVERT: A 738 LEU cc_start: 0.8210 (tt) cc_final: 0.7804 (mm) REVERT: A 759 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8473 (pp) REVERT: A 781 MET cc_start: 0.8411 (tmm) cc_final: 0.7869 (ppp) REVERT: A 879 MET cc_start: 0.7860 (mtt) cc_final: 0.7348 (mtt) REVERT: A 1021 MET cc_start: 0.7570 (tpp) cc_final: 0.7031 (tpp) REVERT: A 1045 PHE cc_start: 0.9012 (t80) cc_final: 0.8790 (t80) REVERT: A 1164 LEU cc_start: 0.9481 (tp) cc_final: 0.9262 (tt) REVERT: C 35 ASN cc_start: 0.9052 (m110) cc_final: 0.8682 (m110) REVERT: C 91 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7135 (tm-30) REVERT: C 97 ASP cc_start: 0.8398 (t0) cc_final: 0.7681 (t0) outliers start: 27 outliers final: 21 residues processed: 171 average time/residue: 0.2389 time to fit residues: 63.6143 Evaluate side-chains 167 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.137691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101333 restraints weight = 30351.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.104899 restraints weight = 16117.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.106284 restraints weight = 10763.429| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14682 Z= 0.170 Angle : 0.634 16.239 20435 Z= 0.304 Chirality : 0.039 0.320 2411 Planarity : 0.003 0.037 2194 Dihedral : 18.988 177.134 3378 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.56 % Allowed : 24.07 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.46 (0.22), residues: 1490 helix: -0.07 (0.21), residues: 605 sheet: -0.56 (0.54), residues: 100 loop : -1.78 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1074 HIS 0.004 0.001 HIS A 328 PHE 0.021 0.001 PHE A 446 TYR 0.014 0.001 TYR A 639 ARG 0.003 0.000 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2633.80 seconds wall clock time: 49 minutes 34.76 seconds (2974.76 seconds total)