Starting phenix.real_space_refine on Thu Mar 14 21:08:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4c_35169/03_2024/8i4c_35169_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4c_35169/03_2024/8i4c_35169.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4c_35169/03_2024/8i4c_35169_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4c_35169/03_2024/8i4c_35169_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4c_35169/03_2024/8i4c_35169_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4c_35169/03_2024/8i4c_35169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4c_35169/03_2024/8i4c_35169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4c_35169/03_2024/8i4c_35169_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4c_35169/03_2024/8i4c_35169_neut_updated.pdb" } resolution = 3.08 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= -0.001 sd= 0.034 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 6337 2.51 5 N 1637 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 GLU 121": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 461": "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 884": "OE1" <-> "OE2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A GLU 1213": "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-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9752 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1219, 9752 Unusual residues: {'PUC': 1} Classifications: {'peptide': 1218, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178, None: 1} Not linked: pdbres="PRO A1298 " pdbres="PUC A1401 " Chain breaks: 2 Time building chain proxies: 5.45, per 1000 atoms: 0.56 Number of scatterers: 9752 At special positions: 0 Unit cell: (75.44, 114.8, 147.6, 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 1637 7.00 C 6337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.6 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: 52 helices and 6 sheets defined 59.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.619A pdb=" N ASN A 28 " --> pdb=" O TRP A 25 " (cutoff:3.500A) Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 53 through 74 Processing helix chain 'A' and resid 80 through 121 removed outlier: 5.199A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 128 through 149 Processing helix chain 'A' and resid 153 through 180 removed outlier: 4.053A pdb=" N HIS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.767A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 232 removed outlier: 4.100A pdb=" N VAL A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR A 209 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N HIS A 213 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 217 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLY A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 4.250A pdb=" N VAL A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 266 through 281 removed outlier: 4.758A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 292 through 341 removed outlier: 4.225A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.921A pdb=" N THR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 Processing helix chain 'A' and resid 451 through 459 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.884A pdb=" N VAL A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 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 567 through 576 Processing helix chain 'A' and resid 581 through 584 removed outlier: 4.030A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.937A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) 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: 3.513A pdb=" N ALA A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 743 removed outlier: 3.931A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 805 Processing helix chain 'A' and resid 810 through 815 Processing helix chain 'A' and resid 818 through 821 No H-bonds generated for 'chain 'A' and resid 818 through 821' Processing helix chain 'A' and resid 827 through 834 removed outlier: 3.666A pdb=" N ASP A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 860 removed outlier: 3.800A pdb=" N ILE A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 867 Proline residue: A 867 - end of helix Processing helix chain 'A' and resid 873 through 883 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 898 through 909 Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 921 through 931 removed outlier: 3.633A pdb=" N GLU A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 965 removed outlier: 4.045A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 1018 removed outlier: 4.362A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1088 Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1156 through 1159 No H-bonds generated for 'chain 'A' and resid 1156 through 1159' 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 1222 Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1268 through 1274 Processing helix chain 'A' and resid 1279 through 1296 Processing sheet with id= A, first strand: chain 'A' and resid 433 through 435 Processing sheet with id= B, first strand: chain 'A' and resid 440 through 443 removed outlier: 6.448A pdb=" N THR A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL A 443 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 559 " --> pdb=" O VAL A 478 " (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 1252 through 1256 removed outlier: 6.794A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1228 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE A1073 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR A1230 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER A1118 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP A1201 " --> pdb=" O SER A1118 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE A1120 " --> pdb=" O ASP A1201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 415 through 417 removed outlier: 8.078A pdb=" N ALA A 417 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN A 429 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 603 through 607 removed outlier: 3.730A pdb=" N GLN A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1377 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: 3.06 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1546 1.30 - 1.43: 2614 1.43 - 1.56: 5732 1.56 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 9962 Sorted by residual: bond pdb=" C12 PUC A1401 " pdb=" C13 PUC A1401 " ideal model delta sigma weight residual 1.704 1.495 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C7 PUC A1401 " pdb=" C8 PUC A1401 " ideal model delta sigma weight residual 1.707 1.523 0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" C21 PUC A1401 " pdb=" C9 PUC A1401 " ideal model delta sigma weight residual 1.347 1.523 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C10 PUC A1401 " pdb=" C9 PUC A1401 " ideal model delta sigma weight residual 1.675 1.519 0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" C12 PUC A1401 " pdb=" C8 PUC A1401 " ideal model delta sigma weight residual 1.384 1.532 -0.148 2.00e-02 2.50e+03 5.51e+01 ... (remaining 9957 not shown) Histogram of bond angle deviations from ideal: 92.05 - 100.45: 10 100.45 - 108.85: 493 108.85 - 117.26: 6639 117.26 - 125.66: 6193 125.66 - 134.06: 161 Bond angle restraints: 13496 Sorted by residual: angle pdb=" C5 PUC A1401 " pdb=" C6 PUC A1401 " pdb=" C7 PUC A1401 " ideal model delta sigma weight residual 152.66 126.18 26.48 3.00e+00 1.11e-01 7.79e+01 angle pdb=" N LEU A 841 " pdb=" CA LEU A 841 " pdb=" C LEU A 841 " ideal model delta sigma weight residual 113.97 103.10 10.87 1.28e+00 6.10e-01 7.21e+01 angle pdb=" C4 PUC A1401 " pdb=" C5 PUC A1401 " pdb=" C6 PUC A1401 " ideal model delta sigma weight residual 112.21 126.80 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" N LEU A 836 " pdb=" CA LEU A 836 " pdb=" C LEU A 836 " ideal model delta sigma weight residual 109.81 120.22 -10.41 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N ARG A 824 " pdb=" CA ARG A 824 " pdb=" C ARG A 824 " ideal model delta sigma weight residual 113.02 107.73 5.29 1.20e+00 6.94e-01 1.95e+01 ... (remaining 13491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5345 17.63 - 35.27: 501 35.27 - 52.90: 91 52.90 - 70.53: 16 70.53 - 88.17: 5 Dihedral angle restraints: 5958 sinusoidal: 2399 harmonic: 3559 Sorted by residual: dihedral pdb=" CA CYS A 253 " pdb=" C CYS A 253 " pdb=" N PHE A 254 " pdb=" CA PHE A 254 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ARG A 398 " pdb=" C ARG A 398 " pdb=" N ASN A 399 " pdb=" CA ASN A 399 " ideal model delta harmonic sigma weight residual 180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG A1220 " pdb=" C ARG A1220 " pdb=" N GLU A1221 " pdb=" CA GLU A1221 " ideal model delta harmonic sigma weight residual -180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.079: 1565 1.079 - 2.158: 0 2.158 - 3.237: 0 3.237 - 4.316: 0 4.316 - 5.395: 1 Chirality restraints: 1566 Sorted by residual: chirality pdb=" C12 PUC A1401 " pdb=" C11 PUC A1401 " pdb=" C13 PUC A1401 " pdb=" C8 PUC A1401 " both_signs ideal model delta sigma weight residual False -2.55 2.85 -5.40 2.00e-01 2.50e+01 7.28e+02 chirality pdb=" C9 PUC A1401 " pdb=" C10 PUC A1401 " pdb=" C21 PUC A1401 " pdb=" C8 PUC A1401 " both_signs ideal model delta sigma weight residual False 2.91 3.19 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA LEU A 835 " pdb=" N LEU A 835 " pdb=" C LEU A 835 " pdb=" CB LEU A 835 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.56e-01 ... (remaining 1563 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 PUC A1401 " -0.213 2.00e-02 2.50e+03 2.11e-01 4.44e+02 pdb=" C5 PUC A1401 " 0.222 2.00e-02 2.50e+03 pdb=" C6 PUC A1401 " 0.200 2.00e-02 2.50e+03 pdb=" C7 PUC A1401 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 PUC A1401 " 0.113 2.00e-02 2.50e+03 1.34e-01 1.79e+02 pdb=" C13 PUC A1401 " -0.067 2.00e-02 2.50e+03 pdb=" C14 PUC A1401 " -0.186 2.00e-02 2.50e+03 pdb=" C15 PUC A1401 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 109 " -0.042 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO A 110 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.035 5.00e-02 4.00e+02 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 813 2.74 - 3.28: 10102 3.28 - 3.82: 16037 3.82 - 4.36: 19345 4.36 - 4.90: 32511 Nonbonded interactions: 78808 Sorted by model distance: nonbonded pdb=" NH1 ARG A 824 " pdb=" CB ARG A1012 " model vdw 2.195 3.520 nonbonded pdb=" OD1 ASP A 953 " pdb=" NE2 GLN A 994 " model vdw 2.234 2.520 nonbonded pdb=" NE2 GLN A1183 " pdb=" O ALA A1203 " model vdw 2.242 2.520 nonbonded pdb=" OG SER A 182 " pdb=" O ASP A 393 " model vdw 2.252 2.440 nonbonded pdb=" O GLN A 580 " pdb=" ND1 HIS A 583 " model vdw 2.256 2.520 ... (remaining 78803 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: 1.850 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: 6.010 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.250 Find NCS groups from input model: 0.270 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 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 : 0.007 0.209 9962 Z= 0.420 Angle : 0.809 26.483 13496 Z= 0.449 Chirality : 0.144 5.395 1566 Planarity : 0.008 0.211 1676 Dihedral : 14.191 88.165 3652 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.13 % Allowed : 0.75 % Favored : 98.12 % 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: -0.96 (0.24), residues: 1212 helix: -0.43 (0.19), residues: 779 sheet: -0.84 (0.59), residues: 76 loop : -0.65 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 89 HIS 0.006 0.001 HIS A1060 PHE 0.020 0.002 PHE A 98 TYR 0.028 0.002 TYR A1016 ARG 0.008 0.001 ARG A1220 *********************** 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 171 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6029 (tp) REVERT: A 157 TYR cc_start: 0.6755 (t80) cc_final: 0.6440 (t80) REVERT: A 200 ASN cc_start: 0.7846 (t0) cc_final: 0.7362 (m-40) REVERT: A 232 GLU cc_start: 0.5712 (mt-10) cc_final: 0.5196 (mt-10) REVERT: A 782 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.6333 (ttp-170) REVERT: A 866 ILE cc_start: 0.7994 (mm) cc_final: 0.7625 (mm) REVERT: A 998 ARG cc_start: 0.5962 (ttp80) cc_final: 0.5601 (tmt170) outliers start: 12 outliers final: 4 residues processed: 169 average time/residue: 0.2744 time to fit residues: 61.4906 Evaluate side-chains 106 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 40.0000 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN A 978 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9962 Z= 0.224 Angle : 0.649 13.571 13496 Z= 0.320 Chirality : 0.044 0.515 1566 Planarity : 0.005 0.051 1676 Dihedral : 6.744 59.579 1343 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.79 % Allowed : 7.72 % Favored : 90.49 % 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: 790 sheet: -0.41 (0.55), residues: 86 loop : -0.29 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 995 HIS 0.004 0.001 HIS A 903 PHE 0.029 0.002 PHE A 324 TYR 0.026 0.002 TYR A1016 ARG 0.006 0.001 ARG A 21 *********************** 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 139 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASN cc_start: 0.7769 (t0) cc_final: 0.7417 (m-40) REVERT: A 241 MET cc_start: 0.7863 (tpp) cc_final: 0.6919 (tpt) REVERT: A 270 ASP cc_start: 0.6943 (m-30) cc_final: 0.6584 (t0) REVERT: A 706 ARG cc_start: 0.6920 (tpt90) cc_final: 0.6655 (tpt90) REVERT: A 782 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.6875 (ttp-170) REVERT: A 909 GLN cc_start: 0.7253 (mt0) cc_final: 0.7002 (pt0) REVERT: A 998 ARG cc_start: 0.6566 (ttp80) cc_final: 0.6349 (ttm110) REVERT: A 1131 MET cc_start: 0.6796 (mmm) cc_final: 0.5688 (mmp) outliers start: 19 outliers final: 11 residues processed: 134 average time/residue: 0.2548 time to fit residues: 46.4583 Evaluate side-chains 114 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 926 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 40.0000 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 0.0670 chunk 74 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN A 845 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 9962 Z= 0.295 Angle : 0.614 8.744 13496 Z= 0.313 Chirality : 0.043 0.219 1566 Planarity : 0.004 0.047 1676 Dihedral : 5.853 57.391 1339 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.45 % Allowed : 10.36 % Favored : 87.19 % 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: -0.28 (0.24), residues: 1212 helix: -0.01 (0.18), residues: 800 sheet: -0.12 (0.56), residues: 82 loop : -0.21 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 89 HIS 0.003 0.001 HIS A 152 PHE 0.025 0.002 PHE A 112 TYR 0.022 0.002 TYR A 881 ARG 0.010 0.001 ARG A1182 *********************** 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 143 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7042 (mm-30) REVERT: A 44 MET cc_start: 0.7202 (tpp) cc_final: 0.6887 (ttm) REVERT: A 241 MET cc_start: 0.8030 (tpp) cc_final: 0.7515 (tpt) REVERT: A 953 ASP cc_start: 0.7408 (m-30) cc_final: 0.7148 (m-30) REVERT: A 1005 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6362 (m110) outliers start: 26 outliers final: 14 residues processed: 133 average time/residue: 0.2193 time to fit residues: 41.7443 Evaluate side-chains 110 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1005 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 104 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9962 Z= 0.222 Angle : 0.541 8.539 13496 Z= 0.273 Chirality : 0.040 0.206 1566 Planarity : 0.003 0.040 1676 Dihedral : 5.309 57.400 1337 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.01 % Allowed : 11.58 % Favored : 85.40 % 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: 0.15 (0.24), residues: 1212 helix: 0.28 (0.19), residues: 797 sheet: 0.05 (0.56), residues: 82 loop : 0.06 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 89 HIS 0.005 0.001 HIS A 153 PHE 0.019 0.002 PHE A 112 TYR 0.016 0.001 TYR A 157 ARG 0.003 0.000 ARG A1132 *********************** 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 132 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.5716 (tm-30) cc_final: 0.5318 (tp40) REVERT: A 241 MET cc_start: 0.8010 (tpp) cc_final: 0.7477 (tpt) REVERT: A 276 MET cc_start: 0.7496 (mmm) cc_final: 0.6749 (mmm) REVERT: A 909 GLN cc_start: 0.8067 (mm110) cc_final: 0.7558 (mt0) REVERT: A 921 GLU cc_start: 0.6579 (pt0) cc_final: 0.6183 (tp30) REVERT: A 936 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: A 953 ASP cc_start: 0.7431 (m-30) cc_final: 0.7144 (m-30) REVERT: A 1131 MET cc_start: 0.6772 (mmm) cc_final: 0.6534 (tpt) outliers start: 32 outliers final: 20 residues processed: 124 average time/residue: 0.2268 time to fit residues: 41.0256 Evaluate side-chains 114 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 801 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1049 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 30.0000 chunk 104 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9962 Z= 0.284 Angle : 0.556 10.404 13496 Z= 0.283 Chirality : 0.041 0.164 1566 Planarity : 0.004 0.040 1676 Dihedral : 5.244 57.501 1337 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.92 % Allowed : 12.15 % Favored : 84.93 % 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: 0.21 (0.24), residues: 1212 helix: 0.31 (0.18), residues: 799 sheet: -0.05 (0.56), residues: 87 loop : 0.19 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 89 HIS 0.007 0.001 HIS A 153 PHE 0.021 0.002 PHE A 112 TYR 0.016 0.002 TYR A 881 ARG 0.002 0.000 ARG A1132 *********************** 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 129 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7016 (mm-30) REVERT: A 66 LYS cc_start: 0.8067 (mttp) cc_final: 0.7853 (mttt) REVERT: A 193 GLN cc_start: 0.5981 (tm-30) cc_final: 0.5516 (tp40) REVERT: A 241 MET cc_start: 0.8045 (tpp) cc_final: 0.7597 (tpt) REVERT: A 276 MET cc_start: 0.7577 (mmm) cc_final: 0.6866 (mmm) REVERT: A 840 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8043 (t80) REVERT: A 909 GLN cc_start: 0.8050 (mm110) cc_final: 0.7487 (mt0) REVERT: A 921 GLU cc_start: 0.6623 (pt0) cc_final: 0.6277 (pm20) REVERT: A 936 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: A 1131 MET cc_start: 0.6864 (mmm) cc_final: 0.6656 (tpt) REVERT: A 1201 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6612 (t0) outliers start: 31 outliers final: 21 residues processed: 124 average time/residue: 0.2053 time to fit residues: 37.2242 Evaluate side-chains 114 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1201 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9962 Z= 0.186 Angle : 0.508 7.530 13496 Z= 0.256 Chirality : 0.039 0.152 1566 Planarity : 0.003 0.038 1676 Dihedral : 5.093 57.737 1337 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.17 % Allowed : 13.75 % 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: 0.48 (0.24), residues: 1212 helix: 0.50 (0.18), residues: 801 sheet: 0.05 (0.55), residues: 87 loop : 0.32 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 89 HIS 0.005 0.001 HIS A 153 PHE 0.019 0.001 PHE A 112 TYR 0.013 0.001 TYR A 881 ARG 0.002 0.000 ARG A1193 *********************** 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 118 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6921 (mm-30) REVERT: A 193 GLN cc_start: 0.5973 (tm-30) cc_final: 0.5474 (tp40) REVERT: A 241 MET cc_start: 0.7952 (tpp) cc_final: 0.7621 (tpt) REVERT: A 276 MET cc_start: 0.7576 (mmm) cc_final: 0.6855 (mmm) REVERT: A 840 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7980 (t80) REVERT: A 883 LEU cc_start: 0.7993 (mt) cc_final: 0.7780 (mm) REVERT: A 909 GLN cc_start: 0.8060 (mm110) cc_final: 0.7479 (mt0) REVERT: A 921 GLU cc_start: 0.6731 (pt0) cc_final: 0.6285 (pm20) REVERT: A 1089 PHE cc_start: 0.8416 (m-10) cc_final: 0.8118 (m-10) outliers start: 23 outliers final: 18 residues processed: 111 average time/residue: 0.2158 time to fit residues: 34.5408 Evaluate side-chains 109 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1049 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9962 Z= 0.172 Angle : 0.499 7.473 13496 Z= 0.252 Chirality : 0.039 0.147 1566 Planarity : 0.003 0.039 1676 Dihedral : 4.966 57.567 1337 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.45 % Allowed : 13.84 % 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: 0.64 (0.24), residues: 1212 helix: 0.66 (0.18), residues: 810 sheet: 0.29 (0.56), residues: 82 loop : 0.22 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 89 HIS 0.005 0.001 HIS A 153 PHE 0.017 0.001 PHE A 112 TYR 0.012 0.001 TYR A 881 ARG 0.002 0.000 ARG A 891 *********************** 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 119 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 193 GLN cc_start: 0.6009 (tm-30) cc_final: 0.5564 (tp40) REVERT: A 241 MET cc_start: 0.7914 (tpp) cc_final: 0.7675 (tpt) REVERT: A 276 MET cc_start: 0.7591 (mmm) cc_final: 0.7349 (mmm) REVERT: A 409 MET cc_start: 0.3040 (ppp) cc_final: 0.2696 (ppp) REVERT: A 822 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8451 (tp) REVERT: A 883 LEU cc_start: 0.7945 (mt) cc_final: 0.7730 (mm) REVERT: A 909 GLN cc_start: 0.8090 (mm110) cc_final: 0.7887 (mm-40) REVERT: A 921 GLU cc_start: 0.6721 (pt0) cc_final: 0.6328 (pm20) REVERT: A 1007 MET cc_start: 0.8234 (mmm) cc_final: 0.7959 (mmm) REVERT: A 1201 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6675 (t0) outliers start: 26 outliers final: 16 residues processed: 110 average time/residue: 0.1847 time to fit residues: 30.8520 Evaluate side-chains 107 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1201 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 0.0980 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 0.0270 chunk 10 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 108 optimal weight: 0.0470 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9962 Z= 0.156 Angle : 0.497 7.955 13496 Z= 0.247 Chirality : 0.039 0.134 1566 Planarity : 0.003 0.035 1676 Dihedral : 4.923 57.711 1337 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.07 % Allowed : 14.41 % Favored : 83.52 % 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: 0.83 (0.24), residues: 1212 helix: 0.86 (0.18), residues: 807 sheet: 0.13 (0.54), residues: 87 loop : 0.18 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 89 HIS 0.005 0.000 HIS A 153 PHE 0.016 0.001 PHE A 112 TYR 0.010 0.001 TYR A 881 ARG 0.003 0.000 ARG A 891 *********************** 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 112 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 193 GLN cc_start: 0.6014 (tm-30) cc_final: 0.5543 (tp40) REVERT: A 276 MET cc_start: 0.7599 (mmm) cc_final: 0.7358 (mmm) REVERT: A 822 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 868 LEU cc_start: 0.7677 (tt) cc_final: 0.7372 (tp) REVERT: A 883 LEU cc_start: 0.7911 (mt) cc_final: 0.7691 (mm) REVERT: A 909 GLN cc_start: 0.8051 (mm110) cc_final: 0.7321 (mt0) REVERT: A 1201 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6647 (t0) outliers start: 22 outliers final: 15 residues processed: 105 average time/residue: 0.2051 time to fit residues: 32.2083 Evaluate side-chains 102 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1201 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.0980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 108 optimal weight: 0.0370 chunk 71 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9962 Z= 0.155 Angle : 0.492 8.215 13496 Z= 0.244 Chirality : 0.038 0.133 1566 Planarity : 0.003 0.034 1676 Dihedral : 4.859 59.529 1337 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.88 % Allowed : 14.69 % Favored : 83.43 % 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: 1.00 (0.25), residues: 1212 helix: 1.02 (0.19), residues: 807 sheet: 0.21 (0.55), residues: 87 loop : 0.15 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 89 HIS 0.005 0.001 HIS A 153 PHE 0.016 0.001 PHE A 112 TYR 0.009 0.001 TYR A 135 ARG 0.004 0.000 ARG A 82 *********************** 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 110 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 193 GLN cc_start: 0.6082 (tm-30) cc_final: 0.5596 (tp40) REVERT: A 409 MET cc_start: 0.3354 (ppp) cc_final: 0.3021 (ppp) REVERT: A 822 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8548 (tp) REVERT: A 840 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7994 (t80) REVERT: A 883 LEU cc_start: 0.7858 (mt) cc_final: 0.7637 (mm) REVERT: A 909 GLN cc_start: 0.8000 (mm110) cc_final: 0.7423 (mt0) REVERT: A 936 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: A 1007 MET cc_start: 0.8208 (mmm) cc_final: 0.7929 (mmm) REVERT: A 1020 GLU cc_start: 0.7380 (tt0) cc_final: 0.7153 (tt0) REVERT: A 1201 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6655 (t0) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.1886 time to fit residues: 30.2371 Evaluate side-chains 105 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1201 ASP 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: 0.8980 chunk 120 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 76 optimal weight: 0.2980 chunk 102 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9962 Z= 0.290 Angle : 0.571 11.776 13496 Z= 0.282 Chirality : 0.041 0.146 1566 Planarity : 0.003 0.033 1676 Dihedral : 4.975 59.980 1337 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.26 % Allowed : 14.60 % Favored : 83.15 % 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: 0.78 (0.24), residues: 1212 helix: 0.80 (0.18), residues: 808 sheet: 0.21 (0.53), residues: 87 loop : 0.19 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 89 HIS 0.008 0.001 HIS A 153 PHE 0.021 0.002 PHE A 336 TYR 0.014 0.001 TYR A 881 ARG 0.006 0.000 ARG A 891 ********************** 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 118 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7052 (mm-30) REVERT: A 193 GLN cc_start: 0.6378 (tm-30) cc_final: 0.5748 (tp40) REVERT: A 200 ASN cc_start: 0.7365 (m-40) cc_final: 0.6934 (m-40) REVERT: A 822 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 840 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7955 (t80) REVERT: A 883 LEU cc_start: 0.7953 (mt) cc_final: 0.7702 (mm) REVERT: A 921 GLU cc_start: 0.6858 (pt0) cc_final: 0.6431 (pm20) REVERT: A 936 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: A 1020 GLU cc_start: 0.7511 (tt0) cc_final: 0.7300 (tt0) REVERT: A 1201 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6731 (t0) outliers start: 24 outliers final: 17 residues processed: 112 average time/residue: 0.1983 time to fit residues: 32.7794 Evaluate side-chains 110 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1201 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 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 = 0.4606 r_free = 0.4606 target = 0.241004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144414 restraints weight = 9751.228| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.58 r_work: 0.3396 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9962 Z= 0.208 Angle : 0.541 10.356 13496 Z= 0.266 Chirality : 0.040 0.191 1566 Planarity : 0.003 0.034 1676 Dihedral : 4.968 58.597 1337 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.88 % Allowed : 14.97 % Favored : 83.15 % 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: 0.88 (0.24), residues: 1212 helix: 0.87 (0.18), residues: 809 sheet: 0.27 (0.53), residues: 87 loop : 0.25 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 89 HIS 0.006 0.001 HIS A 153 PHE 0.018 0.001 PHE A 112 TYR 0.013 0.001 TYR A 881 ARG 0.006 0.000 ARG A 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.44 seconds wall clock time: 43 minutes 7.60 seconds (2587.60 seconds total)