Starting phenix.real_space_refine on Sun Jul 21 12:35:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/07_2024/5vzl_8749_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/07_2024/5vzl_8749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/07_2024/5vzl_8749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/07_2024/5vzl_8749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/07_2024/5vzl_8749_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/07_2024/5vzl_8749_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 25 5.16 5 C 8364 2.51 5 N 2420 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 919": "NH1" <-> "NH2" Residue "A ARG 1114": "NH1" <-> "NH2" Residue "A PHE 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1333": "NH1" <-> "NH2" Residue "A ARG 1335": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13915 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2494 Unusual residues: {'GTP': 1} Classifications: {'RNA': 115, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 18, 'rna3p': 96, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "A" Number of atoms: 10711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10711 Classifications: {'peptide': 1364} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 35, 'TRANS': 1328} Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 220 Chain: "C" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 7.76, per 1000 atoms: 0.56 Number of scatterers: 13915 At special positions: 0 Unit cell: (112.35, 136.96, 120.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 118 15.00 O 2988 8.00 N 2420 7.00 C 8364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.21 Conformation dependent library (CDL) restraints added in 2.2 seconds 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 11 sheets defined 52.0% alpha, 6.6% beta 30 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 removed outlier: 3.556A pdb=" N ARG A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.739A pdb=" N MET A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.866A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.768A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.865A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.859A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 5.253A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 282 No H-bonds generated for 'chain 'A' and resid 281 through 282' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 317 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.506A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.816A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.314A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.709A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.632A pdb=" N VAL A 481 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.904A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 removed outlier: 4.328A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.860A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.579A pdb=" N HIS A 723 " --> pdb=" O SER A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 769 through 773 removed outlier: 3.898A pdb=" N LYS A 772 " --> pdb=" O THR A 769 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 773 " --> pdb=" O THR A 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 769 through 773' Processing helix chain 'A' and resid 776 through 792 Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.620A pdb=" N LYS A 797 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.613A pdb=" N TYR A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 864 removed outlier: 3.593A pdb=" N ARG A 864 " --> pdb=" O ASP A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.708A pdb=" N LYS A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 909 through 921 removed outlier: 3.834A pdb=" N GLN A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.592A pdb=" N ARG A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.822A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.767A pdb=" N GLU A1007 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.850A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1281 removed outlier: 3.974A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A1279 " --> pdb=" O GLU A1275 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A1280 " --> pdb=" O PHE A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.609A pdb=" N HIS A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1314 through 1317 Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.627A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.934A pdb=" N LEU C 6 " --> pdb=" O ASN C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.999A pdb=" N LEU C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 83 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 3.597A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.178A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1050 through 1051 Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 6.267A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.564A pdb=" N GLU A1162 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A1145 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A1166 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.796A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.938A pdb=" N ILE C 43 " --> pdb=" O LEU C 30 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 6.98 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2283 1.32 - 1.44: 4269 1.44 - 1.56: 7579 1.56 - 1.69: 234 1.69 - 1.81: 48 Bond restraints: 14413 Sorted by residual: bond pdb=" C3' A B 47 " pdb=" O3' A B 47 " ideal model delta sigma weight residual 1.427 1.453 -0.026 1.50e-02 4.44e+03 2.90e+00 bond pdb=" C GLY A1319 " pdb=" N ALA A1320 " ideal model delta sigma weight residual 1.340 1.243 0.098 5.87e-02 2.90e+02 2.77e+00 bond pdb=" N9 G B 4 " pdb=" C4 G B 4 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.03e+00 bond pdb=" CB PHE A 972 " pdb=" CG PHE A 972 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.97e+00 ... (remaining 14408 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.82: 770 105.82 - 113.54: 8409 113.54 - 121.26: 7241 121.26 - 128.98: 3473 128.98 - 136.70: 166 Bond angle restraints: 20059 Sorted by residual: angle pdb=" N VAL A1015 " pdb=" CA VAL A1015 " pdb=" C VAL A1015 " ideal model delta sigma weight residual 111.91 106.73 5.18 8.90e-01 1.26e+00 3.38e+01 angle pdb=" C3' A B 47 " pdb=" O3' A B 47 " pdb=" P A B 48 " ideal model delta sigma weight residual 120.20 127.23 -7.03 1.50e+00 4.44e-01 2.20e+01 angle pdb=" CA ARG C 33 " pdb=" CB ARG C 33 " pdb=" CG ARG C 33 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" C PHE A 196 " pdb=" N GLU A 197 " pdb=" CA GLU A 197 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C3' A B 86 " pdb=" O3' A B 86 " pdb=" P A B 87 " ideal model delta sigma weight residual 120.20 126.54 -6.34 1.50e+00 4.44e-01 1.79e+01 ... (remaining 20054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 8449 35.20 - 70.39: 317 70.39 - 105.59: 37 105.59 - 140.78: 4 140.78 - 175.98: 5 Dihedral angle restraints: 8812 sinusoidal: 4546 harmonic: 4266 Sorted by residual: dihedral pdb=" O4' C B 88 " pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sinusoidal sigma weight residual 200.00 39.82 160.18 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U B 7 " pdb=" C1' U B 7 " pdb=" N1 U B 7 " pdb=" C2 U B 7 " ideal model delta sinusoidal sigma weight residual 232.00 56.02 175.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N GLU C 47 " pdb=" CA GLU C 47 " ideal model delta harmonic sigma weight residual 180.00 143.46 36.54 0 5.00e+00 4.00e-02 5.34e+01 ... (remaining 8809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1930 0.062 - 0.125: 377 0.125 - 0.187: 39 0.187 - 0.250: 8 0.250 - 0.312: 2 Chirality restraints: 2356 Sorted by residual: chirality pdb=" C3' C B 35 " pdb=" C4' C B 35 " pdb=" O3' C B 35 " pdb=" C2' C B 35 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C3' A B 47 " pdb=" C4' A B 47 " pdb=" O3' A B 47 " pdb=" C2' A B 47 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" P A B 48 " pdb=" OP1 A B 48 " pdb=" OP2 A B 48 " pdb=" O5' A B 48 " both_signs ideal model delta sigma weight residual True 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2353 not shown) Planarity restraints: 2153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 47 " 0.040 2.00e-02 2.50e+03 1.79e-02 8.80e+00 pdb=" N9 A B 47 " -0.038 2.00e-02 2.50e+03 pdb=" C8 A B 47 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A B 47 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A B 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 47 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 47 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A B 47 " 0.013 2.00e-02 2.50e+03 pdb=" C2 A B 47 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A B 47 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A B 47 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 271 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C TYR A 271 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR A 271 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 272 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1326 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C TYR A1326 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR A1326 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A1327 " 0.016 2.00e-02 2.50e+03 ... (remaining 2150 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2067 2.75 - 3.29: 13382 3.29 - 3.83: 24507 3.83 - 4.36: 27918 4.36 - 4.90: 42797 Nonbonded interactions: 110671 Sorted by model distance: nonbonded pdb=" O2' G B 61 " pdb=" OH TYR A 359 " model vdw 2.216 2.440 nonbonded pdb=" O GLN C 78 " pdb=" OG1 THR C 81 " model vdw 2.239 2.440 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR A 474 " pdb=" OD1 ASN A 477 " model vdw 2.273 2.440 nonbonded pdb=" OG1 THR A 560 " pdb=" OD1 ASP A 585 " model vdw 2.296 2.440 ... (remaining 110666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 43.260 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 14413 Z= 0.366 Angle : 0.958 12.390 20059 Z= 0.508 Chirality : 0.050 0.312 2356 Planarity : 0.006 0.068 2153 Dihedral : 17.273 175.978 6052 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.25 % Allowed : 3.33 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.17), residues: 1447 helix: -2.93 (0.14), residues: 661 sheet: -1.64 (0.49), residues: 110 loop : -2.64 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 464 HIS 0.007 0.002 HIS A1241 PHE 0.020 0.003 PHE A1008 TYR 0.028 0.003 TYR A 973 ARG 0.015 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: -0.3469 (OUTLIER) cc_final: -0.3722 (mpt-90) REVERT: A 642 LEU cc_start: 0.3241 (mm) cc_final: 0.2945 (mm) REVERT: A 643 PHE cc_start: 0.0746 (m-10) cc_final: 0.0429 (m-80) REVERT: A 822 MET cc_start: -0.4326 (mmm) cc_final: -0.5093 (mtt) REVERT: A 1213 MET cc_start: 0.4589 (mtm) cc_final: 0.4064 (ppp) outliers start: 3 outliers final: 0 residues processed: 124 average time/residue: 0.3168 time to fit residues: 55.2964 Evaluate side-chains 82 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 0.0970 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 99 HIS A 137 HIS A 194 GLN A 224 ASN A 501 ASN A 522 ASN A 595 HIS A 609 ASN A 709 GLN A 767 ASN ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN A 899 ASN A1091 GLN A1264 HIS A1286 ASN C 2 ASN C 12 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0616 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14413 Z= 0.186 Angle : 0.619 9.582 20059 Z= 0.318 Chirality : 0.039 0.254 2356 Planarity : 0.005 0.063 2153 Dihedral : 19.915 179.910 3330 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.33 % Allowed : 6.25 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.20), residues: 1447 helix: -0.80 (0.18), residues: 693 sheet: -1.90 (0.41), residues: 135 loop : -2.28 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.009 0.001 HIS A 328 PHE 0.014 0.002 PHE A 164 TYR 0.021 0.002 TYR A 155 ARG 0.007 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.0520 (p) cc_final: 0.0179 (p) REVERT: A 32 PHE cc_start: 0.4200 (OUTLIER) cc_final: 0.3798 (m-10) REVERT: A 161 MET cc_start: 0.2651 (mmm) cc_final: 0.2334 (mmm) REVERT: A 194 GLN cc_start: -0.2936 (OUTLIER) cc_final: -0.3658 (mm-40) REVERT: A 207 ASP cc_start: 0.5674 (t0) cc_final: 0.5073 (p0) REVERT: A 241 LEU cc_start: -0.2785 (OUTLIER) cc_final: -0.3457 (mp) REVERT: A 904 GLU cc_start: 0.3866 (tt0) cc_final: 0.3012 (mt-10) REVERT: A 976 ARG cc_start: 0.0394 (ptp-170) cc_final: -0.0344 (ptt180) REVERT: A 1095 VAL cc_start: -0.1642 (t) cc_final: -0.2117 (p) REVERT: A 1148 LYS cc_start: 0.6734 (pttm) cc_final: 0.6483 (pttm) REVERT: C 31 ILE cc_start: 0.4455 (OUTLIER) cc_final: 0.4220 (pp) outliers start: 16 outliers final: 4 residues processed: 107 average time/residue: 0.2688 time to fit residues: 43.1053 Evaluate side-chains 86 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 95 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS A 807 GLN A 817 GLN A 899 ASN ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 HIS A1308 ASN A1317 ASN C 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0924 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14413 Z= 0.197 Angle : 0.625 11.371 20059 Z= 0.322 Chirality : 0.040 0.225 2356 Planarity : 0.004 0.047 2153 Dihedral : 19.605 178.632 3326 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.17 % Allowed : 8.25 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.21), residues: 1447 helix: -0.11 (0.19), residues: 703 sheet: -0.80 (0.51), residues: 93 loop : -2.26 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 476 HIS 0.010 0.002 HIS A 328 PHE 0.020 0.002 PHE A 704 TYR 0.018 0.002 TYR A 656 ARG 0.006 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.306 Fit side-chains REVERT: A 161 MET cc_start: 0.2947 (mmm) cc_final: 0.2416 (mmm) REVERT: A 207 ASP cc_start: 0.5445 (t0) cc_final: 0.4922 (p0) REVERT: A 241 LEU cc_start: -0.2976 (OUTLIER) cc_final: -0.3545 (mp) REVERT: A 269 ASP cc_start: 0.1101 (OUTLIER) cc_final: 0.0184 (t70) REVERT: A 694 MET cc_start: 0.0108 (ppp) cc_final: -0.2044 (mpp) REVERT: A 904 GLU cc_start: 0.4461 (tt0) cc_final: 0.3622 (mt-10) REVERT: A 970 PHE cc_start: 0.1050 (m-80) cc_final: -0.0159 (m-80) REVERT: A 1060 ARG cc_start: 0.3014 (mtp85) cc_final: 0.2184 (mmm160) REVERT: A 1089 MET cc_start: 0.0246 (tmm) cc_final: -0.0302 (tmm) REVERT: A 1328 ASP cc_start: 0.2095 (p0) cc_final: 0.1629 (t70) REVERT: A 1333 ARG cc_start: 0.0759 (OUTLIER) cc_final: -0.0403 (ptm160) REVERT: C 30 LEU cc_start: -0.4183 (OUTLIER) cc_final: -0.4390 (tp) REVERT: C 31 ILE cc_start: 0.4551 (OUTLIER) cc_final: 0.4233 (pp) REVERT: C 33 ARG cc_start: 0.5012 (mmt90) cc_final: 0.4466 (mmt180) REVERT: C 77 MET cc_start: -0.0716 (mmp) cc_final: -0.1716 (ptt) REVERT: C 80 ILE cc_start: -0.4096 (OUTLIER) cc_final: -0.4683 (pt) outliers start: 26 outliers final: 11 residues processed: 114 average time/residue: 0.2802 time to fit residues: 46.9482 Evaluate side-chains 98 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1333 ARG Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 80 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 149 optimal weight: 0.0170 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 342 GLN A 758 ASN A 899 ASN A 920 GLN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 ASN ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 ASN A1295 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1355 moved from start: 0.7084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14413 Z= 0.272 Angle : 0.793 10.583 20059 Z= 0.409 Chirality : 0.046 0.247 2356 Planarity : 0.006 0.063 2153 Dihedral : 19.853 172.080 3326 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.08 % Allowed : 11.17 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1447 helix: -0.52 (0.19), residues: 689 sheet: -0.86 (0.51), residues: 89 loop : -2.27 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 476 HIS 0.012 0.002 HIS A1264 PHE 0.039 0.003 PHE A 704 TYR 0.026 0.003 TYR A 515 ARG 0.009 0.001 ARG A1122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 104 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ASP cc_start: 0.5685 (t0) cc_final: 0.5347 (p0) REVERT: A 241 LEU cc_start: -0.2745 (OUTLIER) cc_final: -0.3468 (mt) REVERT: A 692 ASN cc_start: -0.4128 (OUTLIER) cc_final: -0.5202 (m-40) REVERT: A 694 MET cc_start: 0.0385 (ppp) cc_final: -0.2169 (mpp) REVERT: A 822 MET cc_start: -0.5068 (mtt) cc_final: -0.5811 (mtp) REVERT: A 904 GLU cc_start: 0.4760 (tt0) cc_final: 0.3813 (mt-10) REVERT: A 970 PHE cc_start: 0.2632 (m-80) cc_final: 0.2124 (m-80) REVERT: A 976 ARG cc_start: 0.2056 (ptp-170) cc_final: -0.0119 (ptt-90) REVERT: A 1060 ARG cc_start: 0.3186 (mtp85) cc_final: 0.2548 (mmm160) REVERT: A 1089 MET cc_start: 0.0408 (tmm) cc_final: -0.0025 (tmm) REVERT: A 1264 HIS cc_start: 0.3529 (t-170) cc_final: 0.3132 (p-80) REVERT: A 1328 ASP cc_start: 0.1392 (p0) cc_final: 0.0998 (t70) REVERT: A 1333 ARG cc_start: 0.2618 (OUTLIER) cc_final: 0.1179 (ptm160) REVERT: C 1 MET cc_start: 0.1759 (ptt) cc_final: -0.0631 (mmt) REVERT: C 33 ARG cc_start: 0.4618 (mmt90) cc_final: 0.4301 (mmt90) outliers start: 37 outliers final: 18 residues processed: 133 average time/residue: 0.2841 time to fit residues: 54.6848 Evaluate side-chains 104 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1333 ARG Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 103 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN A 723 HIS A 758 ASN A1091 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1223 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14413 Z= 0.149 Angle : 0.590 9.636 20059 Z= 0.302 Chirality : 0.039 0.226 2356 Planarity : 0.004 0.048 2153 Dihedral : 19.420 174.554 3326 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.75 % Allowed : 12.08 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1447 helix: 0.13 (0.19), residues: 699 sheet: -0.28 (0.55), residues: 89 loop : -2.00 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 476 HIS 0.005 0.001 HIS A1264 PHE 0.019 0.001 PHE A1204 TYR 0.015 0.001 TYR A 362 ARG 0.006 0.001 ARG A1122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 90 time to evaluate : 1.295 Fit side-chains REVERT: A 119 PHE cc_start: -0.0668 (m-10) cc_final: -0.0928 (m-10) REVERT: A 207 ASP cc_start: 0.5833 (t0) cc_final: 0.5584 (p0) REVERT: A 241 LEU cc_start: -0.3024 (OUTLIER) cc_final: -0.3635 (mt) REVERT: A 401 LYS cc_start: 0.3093 (mmtt) cc_final: 0.2421 (mmmt) REVERT: A 694 MET cc_start: 0.0576 (ppp) cc_final: -0.1867 (mpp) REVERT: A 904 GLU cc_start: 0.5168 (tt0) cc_final: 0.4256 (mt-10) REVERT: A 970 PHE cc_start: 0.2367 (m-80) cc_final: 0.2028 (m-80) REVERT: A 976 ARG cc_start: 0.2112 (ptp-170) cc_final: -0.0148 (ptt-90) REVERT: A 1004 LEU cc_start: -0.1237 (OUTLIER) cc_final: -0.2354 (tp) REVERT: A 1060 ARG cc_start: 0.3139 (mtp85) cc_final: 0.2369 (mmm160) REVERT: A 1264 HIS cc_start: 0.3118 (t-170) cc_final: 0.1843 (p-80) REVERT: A 1268 GLU cc_start: 0.0383 (OUTLIER) cc_final: -0.0147 (tm-30) REVERT: C 1 MET cc_start: 0.1426 (ptt) cc_final: -0.0726 (mmt) REVERT: C 31 ILE cc_start: 0.5561 (OUTLIER) cc_final: 0.5139 (pp) REVERT: C 33 ARG cc_start: 0.4132 (mmt90) cc_final: 0.3770 (mmt180) outliers start: 33 outliers final: 16 residues processed: 118 average time/residue: 0.2833 time to fit residues: 49.2549 Evaluate side-chains 98 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 61 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 0.0770 chunk 144 optimal weight: 4.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 342 GLN A 723 HIS A1091 GLN A1264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1249 moved from start: 0.7784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14413 Z= 0.150 Angle : 0.574 10.259 20059 Z= 0.292 Chirality : 0.038 0.217 2356 Planarity : 0.004 0.048 2153 Dihedral : 19.230 174.577 3326 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.75 % Allowed : 12.58 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1447 helix: 0.46 (0.20), residues: 694 sheet: -0.47 (0.50), residues: 98 loop : -1.86 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 PHE 0.013 0.001 PHE A1204 TYR 0.018 0.002 TYR A1265 ARG 0.005 0.000 ARG A1122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 86 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.5774 (t0) cc_final: 0.5528 (p0) REVERT: A 241 LEU cc_start: -0.3032 (OUTLIER) cc_final: -0.3699 (mt) REVERT: A 269 ASP cc_start: 0.1210 (OUTLIER) cc_final: 0.0234 (t70) REVERT: A 374 LYS cc_start: 0.7383 (tppt) cc_final: 0.7126 (tptm) REVERT: A 648 MET cc_start: -0.3597 (tpt) cc_final: -0.4107 (tpt) REVERT: A 694 MET cc_start: 0.0433 (ppp) cc_final: -0.1990 (mpp) REVERT: A 904 GLU cc_start: 0.5028 (tt0) cc_final: 0.4151 (mt-10) REVERT: A 939 MET cc_start: -0.1638 (ptt) cc_final: -0.2358 (ptp) REVERT: A 970 PHE cc_start: 0.2400 (m-80) cc_final: 0.2081 (m-80) REVERT: A 976 ARG cc_start: 0.2170 (ptp-170) cc_final: -0.0148 (ptt-90) REVERT: A 1060 ARG cc_start: 0.2620 (mtp85) cc_final: 0.1839 (tpt90) REVERT: A 1264 HIS cc_start: 0.2619 (t-90) cc_final: 0.2377 (p90) REVERT: C 33 ARG cc_start: 0.4175 (mmt90) cc_final: 0.3953 (mmt180) REVERT: C 37 ASP cc_start: 0.7224 (t70) cc_final: 0.6385 (m-30) outliers start: 33 outliers final: 17 residues processed: 115 average time/residue: 0.2582 time to fit residues: 44.6889 Evaluate side-chains 100 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1131 TYR Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 61 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 149 optimal weight: 0.0170 chunk 93 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 GLN A1241 HIS ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1433 moved from start: 0.8964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14413 Z= 0.191 Angle : 0.665 10.827 20059 Z= 0.337 Chirality : 0.041 0.228 2356 Planarity : 0.004 0.048 2153 Dihedral : 19.470 172.898 3326 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.08 % Allowed : 13.17 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1447 helix: 0.26 (0.20), residues: 685 sheet: -0.52 (0.52), residues: 98 loop : -1.89 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 476 HIS 0.008 0.002 HIS A 167 PHE 0.018 0.002 PHE A 491 TYR 0.017 0.002 TYR A 362 ARG 0.006 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 132 TYR cc_start: 0.0888 (OUTLIER) cc_final: -0.0536 (m-80) REVERT: A 241 LEU cc_start: -0.3005 (OUTLIER) cc_final: -0.3702 (mt) REVERT: A 252 PHE cc_start: 0.0154 (OUTLIER) cc_final: -0.0355 (m-80) REVERT: A 648 MET cc_start: -0.3562 (tpt) cc_final: -0.3831 (mmm) REVERT: A 694 MET cc_start: 0.0206 (ppp) cc_final: -0.2522 (mpp) REVERT: A 904 GLU cc_start: 0.4972 (tt0) cc_final: 0.4230 (mt-10) REVERT: A 939 MET cc_start: -0.1441 (ptt) cc_final: -0.2196 (ptp) REVERT: A 970 PHE cc_start: 0.3029 (m-80) cc_final: 0.2510 (m-80) REVERT: A 976 ARG cc_start: 0.2268 (ptp-170) cc_final: -0.0102 (ptt-90) REVERT: A 1056 GLU cc_start: 0.1421 (mt-10) cc_final: 0.0954 (tp30) REVERT: A 1060 ARG cc_start: 0.2402 (mtp85) cc_final: 0.1958 (tpt90) REVERT: A 1264 HIS cc_start: 0.2264 (t70) cc_final: 0.1589 (p-80) REVERT: A 1268 GLU cc_start: 0.2134 (OUTLIER) cc_final: 0.0750 (tm-30) REVERT: C 30 LEU cc_start: -0.4484 (OUTLIER) cc_final: -0.4709 (tp) REVERT: C 31 ILE cc_start: 0.5404 (OUTLIER) cc_final: 0.4960 (pt) REVERT: C 37 ASP cc_start: 0.7106 (t70) cc_final: 0.6197 (m-30) REVERT: C 77 MET cc_start: 0.0268 (mmp) cc_final: -0.0410 (ppp) outliers start: 37 outliers final: 19 residues processed: 115 average time/residue: 0.2658 time to fit residues: 45.8325 Evaluate side-chains 102 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1131 TYR Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 61 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 94 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 chunk 135 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A1091 GLN ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1311 moved from start: 0.9050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14413 Z= 0.125 Angle : 0.559 10.571 20059 Z= 0.283 Chirality : 0.038 0.221 2356 Planarity : 0.003 0.046 2153 Dihedral : 19.195 176.889 3326 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.83 % Allowed : 14.25 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1447 helix: 0.64 (0.20), residues: 685 sheet: -0.56 (0.53), residues: 96 loop : -1.77 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.005 0.001 HIS A 412 PHE 0.028 0.001 PHE A 119 TYR 0.019 0.001 TYR A 325 ARG 0.003 0.000 ARG A1122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: -0.3164 (OUTLIER) cc_final: -0.3807 (mt) REVERT: A 631 MET cc_start: -0.0429 (mmm) cc_final: -0.1231 (mmm) REVERT: A 692 ASN cc_start: -0.3679 (OUTLIER) cc_final: -0.4665 (m-40) REVERT: A 694 MET cc_start: 0.0133 (ppp) cc_final: -0.2477 (mpp) REVERT: A 904 GLU cc_start: 0.5056 (tt0) cc_final: 0.4338 (mt-10) REVERT: A 939 MET cc_start: -0.1096 (ptt) cc_final: -0.1846 (ptp) REVERT: A 970 PHE cc_start: 0.2677 (m-80) cc_final: 0.2107 (m-80) REVERT: A 976 ARG cc_start: 0.2093 (ptp-170) cc_final: -0.0315 (ptt-90) REVERT: A 1056 GLU cc_start: 0.1605 (mt-10) cc_final: 0.1165 (tp30) REVERT: A 1060 ARG cc_start: 0.2343 (mtp85) cc_final: 0.1851 (tpt90) REVERT: A 1264 HIS cc_start: 0.1838 (t70) cc_final: 0.1178 (p-80) REVERT: A 1268 GLU cc_start: 0.1851 (OUTLIER) cc_final: 0.0416 (tm-30) REVERT: C 1 MET cc_start: 0.2135 (ptt) cc_final: -0.0586 (tpt) REVERT: C 37 ASP cc_start: 0.7227 (t70) cc_final: 0.6501 (m-30) REVERT: C 77 MET cc_start: 0.0195 (mmp) cc_final: -0.0572 (ptt) outliers start: 22 outliers final: 13 residues processed: 97 average time/residue: 0.2537 time to fit residues: 37.4781 Evaluate side-chains 89 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 61 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 91 optimal weight: 0.0970 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 609 ASN A 612 ASN ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1517 moved from start: 0.9854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 14413 Z= 0.208 Angle : 0.670 10.693 20059 Z= 0.341 Chirality : 0.041 0.220 2356 Planarity : 0.004 0.048 2153 Dihedral : 19.411 174.555 3326 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.67 % Allowed : 13.75 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.22), residues: 1447 helix: 0.27 (0.20), residues: 684 sheet: -1.16 (0.50), residues: 107 loop : -1.83 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 476 HIS 0.010 0.002 HIS A 412 PHE 0.025 0.002 PHE A 119 TYR 0.016 0.002 TYR A 362 ARG 0.005 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 78 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: A 132 TYR cc_start: 0.1226 (OUTLIER) cc_final: -0.0071 (m-80) REVERT: A 241 LEU cc_start: -0.3000 (OUTLIER) cc_final: -0.3701 (mt) REVERT: A 354 GLN cc_start: -0.1950 (OUTLIER) cc_final: -0.2267 (mt0) REVERT: A 904 GLU cc_start: 0.5194 (tt0) cc_final: 0.4578 (mt-10) REVERT: A 970 PHE cc_start: 0.2810 (m-80) cc_final: 0.2271 (m-80) REVERT: A 976 ARG cc_start: 0.2188 (ptp-170) cc_final: -0.0171 (ptt-90) REVERT: A 1056 GLU cc_start: 0.1795 (mt-10) cc_final: 0.1512 (tp30) REVERT: A 1060 ARG cc_start: 0.2226 (mtp85) cc_final: 0.1752 (tpt90) REVERT: A 1264 HIS cc_start: 0.2378 (t70) cc_final: 0.2059 (t70) REVERT: A 1268 GLU cc_start: 0.1767 (OUTLIER) cc_final: 0.0847 (tm-30) REVERT: C 37 ASP cc_start: 0.7171 (t70) cc_final: 0.6549 (m-30) REVERT: C 77 MET cc_start: 0.0240 (mmp) cc_final: -0.0556 (ppp) outliers start: 32 outliers final: 19 residues processed: 105 average time/residue: 0.2821 time to fit residues: 44.1301 Evaluate side-chains 98 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1131 TYR Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 61 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 75 optimal weight: 0.0030 chunk 97 optimal weight: 6.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 309 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 415 HIS ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1447 moved from start: 1.0044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14413 Z= 0.148 Angle : 0.598 9.922 20059 Z= 0.303 Chirality : 0.039 0.202 2356 Planarity : 0.004 0.047 2153 Dihedral : 19.284 175.808 3326 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.08 % Allowed : 14.50 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1447 helix: 0.48 (0.20), residues: 682 sheet: -0.91 (0.55), residues: 96 loop : -1.86 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.013 0.001 HIS A1241 PHE 0.030 0.002 PHE A 119 TYR 0.017 0.001 TYR A 325 ARG 0.003 0.000 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 132 TYR cc_start: 0.1434 (OUTLIER) cc_final: 0.0183 (m-80) REVERT: A 241 LEU cc_start: -0.3186 (OUTLIER) cc_final: -0.3793 (mt) REVERT: A 631 MET cc_start: -0.0896 (mmm) cc_final: -0.1674 (mmm) REVERT: A 904 GLU cc_start: 0.4958 (tt0) cc_final: 0.4414 (mt-10) REVERT: A 939 MET cc_start: -0.1620 (ptt) cc_final: -0.2425 (ptp) REVERT: A 970 PHE cc_start: 0.2600 (m-80) cc_final: 0.2148 (m-80) REVERT: A 976 ARG cc_start: 0.2192 (ptp-170) cc_final: -0.0175 (ptt-90) REVERT: A 1056 GLU cc_start: 0.2032 (mt-10) cc_final: 0.1720 (tp30) REVERT: A 1060 ARG cc_start: 0.2201 (mtp85) cc_final: 0.1710 (tpt90) REVERT: A 1264 HIS cc_start: 0.2705 (t70) cc_final: 0.2319 (t70) REVERT: A 1268 GLU cc_start: 0.1710 (OUTLIER) cc_final: 0.0834 (tm-30) REVERT: C 1 MET cc_start: 0.2006 (ptt) cc_final: -0.0736 (mmt) REVERT: C 33 ARG cc_start: 0.4607 (mmt90) cc_final: 0.3455 (mpt-90) REVERT: C 37 ASP cc_start: 0.7272 (t70) cc_final: 0.6575 (m-30) REVERT: C 71 GLU cc_start: -0.1966 (OUTLIER) cc_final: -0.2842 (pm20) REVERT: C 77 MET cc_start: 0.0159 (mmp) cc_final: -0.0380 (ppp) outliers start: 25 outliers final: 17 residues processed: 103 average time/residue: 0.2517 time to fit residues: 39.9298 Evaluate side-chains 99 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 754 HIS ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.264495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.228814 restraints weight = 30562.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.233482 restraints weight = 17371.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.236684 restraints weight = 11307.980| |-----------------------------------------------------------------------------| r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1821 moved from start: 1.0256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14413 Z= 0.142 Angle : 0.588 8.007 20059 Z= 0.299 Chirality : 0.039 0.275 2356 Planarity : 0.004 0.045 2153 Dihedral : 19.167 174.620 3326 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.67 % Allowed : 15.17 % Favored : 83.17 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1447 helix: 0.58 (0.20), residues: 682 sheet: -0.89 (0.55), residues: 96 loop : -1.78 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.022 0.002 HIS A 412 PHE 0.028 0.002 PHE A 119 TYR 0.028 0.001 TYR A1237 ARG 0.004 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2496.95 seconds wall clock time: 45 minutes 29.86 seconds (2729.86 seconds total)