Starting phenix.real_space_refine on Thu Jan 18 23:23:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/01_2024/8j3w_35967_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/01_2024/8j3w_35967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/01_2024/8j3w_35967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/01_2024/8j3w_35967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/01_2024/8j3w_35967_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3w_35967/01_2024/8j3w_35967_neut_updated.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6325 2.51 5 N 1636 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 1004": "OE1" <-> "OE2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1140": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A GLU 1213": "OE1" <-> "OE2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A GLU 1254": "OE1" <-> "OE2" Residue "A GLU 1257": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A GLU 1280": "OE1" <-> "OE2" Residue "A GLU 1286": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9739 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1219, 9739 Unusual residues: {'AIN': 1} Classifications: {'peptide': 1218, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178, None: 1} Not linked: pdbres="PRO A1298 " pdbres="AIN A1401 " Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 5.74, per 1000 atoms: 0.59 Number of scatterers: 9739 At special positions: 0 Unit cell: (72.98, 114.8, 141.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1735 8.00 N 1636 7.00 C 6325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 4 sheets defined 64.4% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 25 through 36 Proline residue: A 29 - end of helix removed outlier: 3.853A pdb=" N LYS A 32 " --> pdb=" O PRO A 29 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS A 35 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A 36 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 74 Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 90 through 121 removed outlier: 3.607A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.872A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 149 Processing helix chain 'A' and resid 151 through 180 Processing helix chain 'A' and resid 183 through 186 No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.645A pdb=" N LEU A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 removed outlier: 4.285A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 211' Processing helix chain 'A' and resid 214 through 281 Proline residue: A 219 - end of helix removed outlier: 8.858A pdb=" N ILE A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.644A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 292 through 336 removed outlier: 3.550A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 Processing helix chain 'A' and resid 369 through 391 Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 501 through 511 removed outlier: 3.851A pdb=" N CYS A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 537 through 551 Processing helix chain 'A' and resid 561 through 564 removed outlier: 4.073A pdb=" N ALA A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 561 through 564' Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.836A pdb=" N LYS A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 594 through 599' Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 627 through 631 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.675A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 743 removed outlier: 3.932A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 806 Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 818 through 833 removed outlier: 3.986A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 860 Processing helix chain 'A' and resid 862 through 888 Proline residue: A 867 - end of helix Proline residue: A 870 - end of helix removed outlier: 3.763A pdb=" N PHE A 882 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 883 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A 884 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER A 886 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 887 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 895 No H-bonds generated for 'chain 'A' and resid 892 through 895' Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.613A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 922 through 970 removed outlier: 3.529A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 1017 removed outlier: 3.503A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 Processing helix chain 'A' and resid 1110 through 1114 Processing helix chain 'A' and resid 1131 through 1136 Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1156 through 1160 Processing helix chain 'A' and resid 1172 through 1174 No H-bonds generated for 'chain 'A' and resid 1172 through 1174' Processing helix chain 'A' and resid 1179 through 1193 Processing helix chain 'A' and resid 1209 through 1225 removed outlier: 4.171A pdb=" N ALA A1224 " --> pdb=" O ARG A1220 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS A1225 " --> pdb=" O GLU A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1238 Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1268 through 1276 removed outlier: 3.732A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1296 Processing sheet with id= A, first strand: chain 'A' and resid 468 through 472 Processing sheet with id= B, first strand: chain 'A' and resid 610 through 615 removed outlier: 6.880A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THR A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 443 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLY A 445 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id= D, first strand: chain 'A' and resid 1251 through 1256 removed outlier: 6.917A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A1228 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A1073 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR A1230 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER A1118 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP A1201 " --> pdb=" O SER A1118 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A1120 " --> pdb=" O ASP A1201 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1547 1.31 - 1.43: 2627 1.43 - 1.56: 5704 1.56 - 1.68: 0 1.68 - 1.81: 70 Bond restraints: 9948 Sorted by residual: bond pdb=" C8 AIN A1401 " pdb=" O3 AIN A1401 " ideal model delta sigma weight residual 1.346 1.398 -0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" CE LYS A1097 " pdb=" NZ LYS A1097 " ideal model delta sigma weight residual 1.489 1.433 0.056 3.00e-02 1.11e+03 3.54e+00 bond pdb=" C8 AIN A1401 " pdb=" C9 AIN A1401 " ideal model delta sigma weight residual 1.495 1.527 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" CB LYS A1097 " pdb=" CG LYS A1097 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" C2 AIN A1401 " pdb=" O3 AIN A1401 " ideal model delta sigma weight residual 1.377 1.400 -0.023 2.00e-02 2.50e+03 1.27e+00 ... (remaining 9943 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 214 106.41 - 113.31: 5574 113.31 - 120.22: 3705 120.22 - 127.13: 3872 127.13 - 134.03: 114 Bond angle restraints: 13479 Sorted by residual: angle pdb=" N VAL A 889 " pdb=" CA VAL A 889 " pdb=" C VAL A 889 " ideal model delta sigma weight residual 111.45 107.82 3.63 9.30e-01 1.16e+00 1.53e+01 angle pdb=" C TYR A 917 " pdb=" N LYS A 918 " pdb=" CA LYS A 918 " ideal model delta sigma weight residual 122.07 115.69 6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N ILE A 969 " pdb=" CA ILE A 969 " pdb=" C ILE A 969 " ideal model delta sigma weight residual 112.98 108.42 4.56 1.25e+00 6.40e-01 1.33e+01 angle pdb=" N ASP A 405 " pdb=" CA ASP A 405 " pdb=" C ASP A 405 " ideal model delta sigma weight residual 112.97 109.41 3.56 1.06e+00 8.90e-01 1.13e+01 angle pdb=" C9 AIN A1401 " pdb=" C8 AIN A1401 " pdb=" O3 AIN A1401 " ideal model delta sigma weight residual 110.82 120.63 -9.81 3.00e+00 1.11e-01 1.07e+01 ... (remaining 13474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5361 17.31 - 34.62: 475 34.62 - 51.93: 83 51.93 - 69.24: 15 69.24 - 86.55: 11 Dihedral angle restraints: 5945 sinusoidal: 2386 harmonic: 3559 Sorted by residual: dihedral pdb=" CA PHE A 336 " pdb=" C PHE A 336 " pdb=" N THR A 337 " pdb=" CA THR A 337 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA PHE A 352 " pdb=" C PHE A 352 " pdb=" N VAL A 353 " pdb=" CA VAL A 353 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA PHE A 418 " pdb=" C PHE A 418 " pdb=" N TRP A 419 " pdb=" CA TRP A 419 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1116 0.037 - 0.074: 333 0.074 - 0.110: 91 0.110 - 0.147: 17 0.147 - 0.184: 4 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CG LEU A1104 " pdb=" CB LEU A1104 " pdb=" CD1 LEU A1104 " pdb=" CD2 LEU A1104 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE A 861 " pdb=" N ILE A 861 " pdb=" C ILE A 861 " pdb=" CB ILE A 861 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA ILE A1231 " pdb=" N ILE A1231 " pdb=" C ILE A1231 " pdb=" CB ILE A1231 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 1558 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 109 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO A 110 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 28 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 29 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 836 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 837 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 837 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 837 " 0.028 5.00e-02 4.00e+02 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 96 2.49 - 3.09: 7696 3.09 - 3.70: 15333 3.70 - 4.30: 23252 4.30 - 4.90: 37644 Nonbonded interactions: 84021 Sorted by model distance: nonbonded pdb=" OG1 THR A 99 " pdb=" OH TYR A 155 " model vdw 1.891 2.440 nonbonded pdb=" OG SER A 570 " pdb=" OH TYR A 596 " model vdw 1.933 2.440 nonbonded pdb=" O THR A 488 " pdb=" OG SER A 491 " model vdw 1.959 2.440 nonbonded pdb=" O ILE A 331 " pdb=" OG1 THR A 335 " model vdw 1.991 2.440 nonbonded pdb=" OE2 GLU A 102 " pdb=" ND1 HIS A 152 " model vdw 2.007 2.520 ... (remaining 84016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.200 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.810 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9948 Z= 0.234 Angle : 0.679 9.810 13479 Z= 0.411 Chirality : 0.039 0.184 1561 Planarity : 0.005 0.075 1676 Dihedral : 13.932 86.553 3639 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.23), residues: 1212 helix: -1.18 (0.17), residues: 788 sheet: -0.75 (0.62), residues: 64 loop : -1.05 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1147 HIS 0.017 0.002 HIS A 213 PHE 0.019 0.002 PHE A 352 TYR 0.018 0.002 TYR A 917 ARG 0.006 0.001 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7423 (tt0) cc_final: 0.6672 (pt0) REVERT: A 288 MET cc_start: 0.8040 (mtt) cc_final: 0.7806 (mtp) REVERT: A 296 SER cc_start: 0.8582 (t) cc_final: 0.8264 (p) REVERT: A 301 ASN cc_start: 0.7845 (m110) cc_final: 0.7362 (m110) REVERT: A 409 MET cc_start: 0.6203 (ppp) cc_final: 0.5847 (mpp) REVERT: A 893 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7519 (tm-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1993 time to fit residues: 41.1192 Evaluate side-chains 116 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 50.0000 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 710 HIS A 903 HIS ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 9948 Z= 0.400 Angle : 0.684 8.569 13479 Z= 0.358 Chirality : 0.044 0.154 1561 Planarity : 0.005 0.073 1676 Dihedral : 5.483 28.999 1318 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.85 % Allowed : 7.25 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.33 (0.23), residues: 1212 helix: -0.75 (0.17), residues: 786 sheet: -0.75 (0.59), residues: 74 loop : -0.75 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 947 HIS 0.014 0.002 HIS A 213 PHE 0.032 0.002 PHE A 352 TYR 0.020 0.002 TYR A 157 ARG 0.006 0.001 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7709 (tt0) cc_final: 0.7277 (tt0) REVERT: A 296 SER cc_start: 0.8715 (t) cc_final: 0.8292 (p) REVERT: A 301 ASN cc_start: 0.7872 (m110) cc_final: 0.7352 (m110) REVERT: A 363 LEU cc_start: 0.7917 (mm) cc_final: 0.7586 (mm) REVERT: A 818 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 893 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7545 (tm-30) outliers start: 9 outliers final: 4 residues processed: 124 average time/residue: 0.2093 time to fit residues: 39.0662 Evaluate side-chains 120 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 20.0000 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9948 Z= 0.217 Angle : 0.557 6.062 13479 Z= 0.295 Chirality : 0.040 0.161 1561 Planarity : 0.005 0.063 1676 Dihedral : 5.025 28.151 1318 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.41 % Allowed : 8.57 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1212 helix: -0.13 (0.18), residues: 781 sheet: -0.42 (0.57), residues: 76 loop : -0.57 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 947 HIS 0.011 0.001 HIS A 934 PHE 0.021 0.002 PHE A 352 TYR 0.018 0.002 TYR A 157 ARG 0.004 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7600 (tt0) cc_final: 0.6947 (tt0) REVERT: A 291 TRP cc_start: 0.8121 (m-10) cc_final: 0.7121 (m-90) REVERT: A 296 SER cc_start: 0.8640 (t) cc_final: 0.8241 (p) REVERT: A 301 ASN cc_start: 0.7852 (m110) cc_final: 0.7352 (m110) REVERT: A 363 LEU cc_start: 0.7890 (mm) cc_final: 0.7565 (mm) REVERT: A 744 MET cc_start: 0.6264 (tpp) cc_final: 0.6062 (mpp) REVERT: A 818 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7830 (mt) REVERT: A 833 ASP cc_start: 0.7897 (m-30) cc_final: 0.7604 (m-30) outliers start: 15 outliers final: 5 residues processed: 134 average time/residue: 0.1983 time to fit residues: 39.5418 Evaluate side-chains 122 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9948 Z= 0.282 Angle : 0.570 7.779 13479 Z= 0.297 Chirality : 0.041 0.148 1561 Planarity : 0.005 0.064 1676 Dihedral : 4.881 28.376 1318 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.69 % Allowed : 10.36 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1212 helix: 0.04 (0.18), residues: 785 sheet: -0.14 (0.58), residues: 76 loop : -0.56 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.024 0.002 PHE A 352 TYR 0.013 0.002 TYR A 157 ARG 0.004 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.001 Fit side-chains REVERT: A 102 GLU cc_start: 0.7646 (tt0) cc_final: 0.6751 (pt0) REVERT: A 247 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7074 (mm) REVERT: A 291 TRP cc_start: 0.8066 (m-10) cc_final: 0.7025 (m-90) REVERT: A 296 SER cc_start: 0.8667 (t) cc_final: 0.8252 (p) REVERT: A 301 ASN cc_start: 0.7884 (m110) cc_final: 0.7355 (m110) REVERT: A 363 LEU cc_start: 0.7971 (mm) cc_final: 0.7558 (mm) REVERT: A 744 MET cc_start: 0.5975 (tpp) cc_final: 0.5758 (mpp) REVERT: A 818 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7817 (mt) REVERT: A 833 ASP cc_start: 0.7865 (m-30) cc_final: 0.7605 (m-30) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 0.1947 time to fit residues: 39.4551 Evaluate side-chains 125 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 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 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9948 Z= 0.218 Angle : 0.558 10.628 13479 Z= 0.288 Chirality : 0.040 0.143 1561 Planarity : 0.004 0.060 1676 Dihedral : 4.755 27.897 1318 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.26 % Allowed : 11.30 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1212 helix: 0.27 (0.18), residues: 786 sheet: -0.11 (0.59), residues: 76 loop : -0.49 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 947 HIS 0.009 0.001 HIS A 934 PHE 0.020 0.002 PHE A 352 TYR 0.014 0.002 TYR A 92 ARG 0.005 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7578 (tt0) cc_final: 0.6803 (pt0) REVERT: A 247 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7171 (mm) REVERT: A 296 SER cc_start: 0.8655 (t) cc_final: 0.8238 (p) REVERT: A 301 ASN cc_start: 0.7885 (m110) cc_final: 0.7331 (m110) REVERT: A 363 LEU cc_start: 0.7948 (mm) cc_final: 0.7554 (mm) REVERT: A 744 MET cc_start: 0.6061 (tpp) cc_final: 0.5830 (mpp) REVERT: A 818 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7812 (mt) outliers start: 24 outliers final: 13 residues processed: 144 average time/residue: 0.1965 time to fit residues: 41.8788 Evaluate side-chains 131 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9948 Z= 0.238 Angle : 0.571 15.600 13479 Z= 0.291 Chirality : 0.041 0.194 1561 Planarity : 0.004 0.061 1676 Dihedral : 4.689 27.508 1318 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.26 % Allowed : 12.15 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1212 helix: 0.35 (0.19), residues: 784 sheet: -0.11 (0.60), residues: 77 loop : -0.43 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.021 0.002 PHE A 352 TYR 0.013 0.002 TYR A 92 ARG 0.006 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.075 Fit side-chains REVERT: A 102 GLU cc_start: 0.7619 (tt0) cc_final: 0.6669 (pt0) REVERT: A 109 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6763 (tt0) REVERT: A 247 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7207 (mm) REVERT: A 291 TRP cc_start: 0.8120 (m-10) cc_final: 0.7069 (m-90) REVERT: A 296 SER cc_start: 0.8634 (t) cc_final: 0.8222 (p) REVERT: A 301 ASN cc_start: 0.7892 (m110) cc_final: 0.7334 (m110) REVERT: A 363 LEU cc_start: 0.7962 (mm) cc_final: 0.7552 (mm) REVERT: A 744 MET cc_start: 0.6103 (tpp) cc_final: 0.5873 (mpp) REVERT: A 818 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7825 (mt) outliers start: 24 outliers final: 17 residues processed: 139 average time/residue: 0.1920 time to fit residues: 39.0926 Evaluate side-chains 140 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.0070 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9948 Z= 0.181 Angle : 0.539 9.254 13479 Z= 0.278 Chirality : 0.040 0.191 1561 Planarity : 0.004 0.060 1676 Dihedral : 4.497 26.012 1318 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.98 % Allowed : 12.90 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1212 helix: 0.60 (0.19), residues: 779 sheet: 0.15 (0.59), residues: 82 loop : -0.15 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 947 HIS 0.009 0.001 HIS A 934 PHE 0.016 0.001 PHE A 495 TYR 0.014 0.001 TYR A 92 ARG 0.004 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.190 Fit side-chains REVERT: A 102 GLU cc_start: 0.7547 (tt0) cc_final: 0.6788 (pt0) REVERT: A 109 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6711 (tt0) REVERT: A 247 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7287 (mm) REVERT: A 291 TRP cc_start: 0.8084 (m-10) cc_final: 0.6989 (m-90) REVERT: A 296 SER cc_start: 0.8600 (t) cc_final: 0.8182 (p) REVERT: A 301 ASN cc_start: 0.7871 (m110) cc_final: 0.7319 (m110) REVERT: A 363 LEU cc_start: 0.7861 (mm) cc_final: 0.7486 (mm) REVERT: A 744 MET cc_start: 0.6071 (tpp) cc_final: 0.5855 (mpp) REVERT: A 818 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7806 (mt) outliers start: 21 outliers final: 16 residues processed: 135 average time/residue: 0.2002 time to fit residues: 39.7947 Evaluate side-chains 138 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9948 Z= 0.260 Angle : 0.567 8.599 13479 Z= 0.292 Chirality : 0.041 0.207 1561 Planarity : 0.004 0.061 1676 Dihedral : 4.515 27.107 1318 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.79 % Allowed : 13.56 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1212 helix: 0.57 (0.19), residues: 780 sheet: 0.28 (0.60), residues: 83 loop : -0.11 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 947 HIS 0.008 0.001 HIS A 934 PHE 0.020 0.002 PHE A 352 TYR 0.012 0.001 TYR A 92 ARG 0.008 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.223 Fit side-chains REVERT: A 102 GLU cc_start: 0.7593 (tt0) cc_final: 0.6737 (pt0) REVERT: A 109 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6824 (tt0) REVERT: A 247 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7235 (mm) REVERT: A 291 TRP cc_start: 0.8083 (m-10) cc_final: 0.7007 (m-90) REVERT: A 296 SER cc_start: 0.8622 (t) cc_final: 0.8197 (p) REVERT: A 301 ASN cc_start: 0.7879 (m110) cc_final: 0.7300 (m110) REVERT: A 363 LEU cc_start: 0.7972 (mm) cc_final: 0.7571 (mm) REVERT: A 744 MET cc_start: 0.6109 (tpp) cc_final: 0.5873 (mpp) REVERT: A 818 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7799 (mt) REVERT: A 1183 GLN cc_start: 0.8444 (tp-100) cc_final: 0.7927 (mt0) outliers start: 19 outliers final: 16 residues processed: 130 average time/residue: 0.1937 time to fit residues: 37.4127 Evaluate side-chains 136 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9948 Z= 0.204 Angle : 0.553 9.555 13479 Z= 0.282 Chirality : 0.040 0.194 1561 Planarity : 0.004 0.059 1676 Dihedral : 4.436 26.360 1318 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.60 % Allowed : 14.31 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1212 helix: 0.66 (0.19), residues: 784 sheet: 0.31 (0.60), residues: 83 loop : -0.10 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 947 HIS 0.009 0.001 HIS A 934 PHE 0.018 0.001 PHE A 352 TYR 0.014 0.001 TYR A 92 ARG 0.008 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.084 Fit side-chains REVERT: A 102 GLU cc_start: 0.7589 (tt0) cc_final: 0.6877 (pt0) REVERT: A 109 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6651 (tt0) REVERT: A 247 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7282 (mm) REVERT: A 291 TRP cc_start: 0.8042 (m-10) cc_final: 0.7011 (m-90) REVERT: A 296 SER cc_start: 0.8615 (t) cc_final: 0.8166 (p) REVERT: A 301 ASN cc_start: 0.7851 (m110) cc_final: 0.7289 (m110) REVERT: A 363 LEU cc_start: 0.7940 (mm) cc_final: 0.7551 (mm) REVERT: A 744 MET cc_start: 0.6139 (tpp) cc_final: 0.5932 (mpp) REVERT: A 818 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7835 (mt) REVERT: A 1183 GLN cc_start: 0.8427 (tp-100) cc_final: 0.7888 (mt0) outliers start: 17 outliers final: 14 residues processed: 135 average time/residue: 0.1896 time to fit residues: 37.6737 Evaluate side-chains 136 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9948 Z= 0.247 Angle : 0.579 10.758 13479 Z= 0.296 Chirality : 0.041 0.240 1561 Planarity : 0.004 0.060 1676 Dihedral : 4.455 26.759 1318 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.69 % Allowed : 14.69 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1212 helix: 0.63 (0.18), residues: 787 sheet: 0.38 (0.60), residues: 83 loop : -0.10 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1025 HIS 0.008 0.001 HIS A 934 PHE 0.019 0.001 PHE A 352 TYR 0.013 0.001 TYR A 92 ARG 0.008 0.000 ARG A 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.050 Fit side-chains REVERT: A 102 GLU cc_start: 0.7627 (tt0) cc_final: 0.6814 (pt0) REVERT: A 109 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6758 (tt0) REVERT: A 247 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7277 (mm) REVERT: A 291 TRP cc_start: 0.8035 (m-10) cc_final: 0.6991 (m-90) REVERT: A 296 SER cc_start: 0.8625 (t) cc_final: 0.8156 (p) REVERT: A 301 ASN cc_start: 0.7860 (m110) cc_final: 0.7281 (m110) REVERT: A 363 LEU cc_start: 0.7958 (mm) cc_final: 0.7553 (mm) REVERT: A 392 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8437 (mp) REVERT: A 744 MET cc_start: 0.6208 (tpp) cc_final: 0.5985 (mpp) REVERT: A 818 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7822 (mt) REVERT: A 1183 GLN cc_start: 0.8426 (tp-100) cc_final: 0.7890 (mt0) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 0.2069 time to fit residues: 40.0511 Evaluate side-chains 133 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.0000 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.246230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.192857 restraints weight = 11229.596| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 3.18 r_work: 0.3721 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9948 Z= 0.197 Angle : 0.554 12.148 13479 Z= 0.281 Chirality : 0.040 0.240 1561 Planarity : 0.004 0.060 1676 Dihedral : 4.345 25.867 1318 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.79 % Allowed : 14.50 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1212 helix: 0.77 (0.18), residues: 785 sheet: 0.40 (0.60), residues: 83 loop : -0.07 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1025 HIS 0.009 0.001 HIS A 934 PHE 0.017 0.001 PHE A 352 TYR 0.014 0.001 TYR A 92 ARG 0.008 0.000 ARG A 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.03 seconds wall clock time: 43 minutes 9.47 seconds (2589.47 seconds total)