Starting phenix.real_space_refine on Sat Aug 23 08:55:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ap1_15556/08_2025/8ap1_15556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ap1_15556/08_2025/8ap1_15556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ap1_15556/08_2025/8ap1_15556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ap1_15556/08_2025/8ap1_15556.map" model { file = "/net/cci-nas-00/data/ceres_data/8ap1_15556/08_2025/8ap1_15556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ap1_15556/08_2025/8ap1_15556.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.016 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: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 7001 2.51 5 N 1939 2.21 5 O 2185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11221 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2781 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 319} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7275 Classifications: {'peptide': 918} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 44, 'TRANS': 873} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'GLU:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "N" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 561 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 539 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 0.23 Number of scatterers: 11221 At special positions: 0 Unit cell: (104.88, 110.96, 113.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 60 15.00 Mg 1 11.99 O 2185 8.00 N 1939 7.00 C 7001 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 - 3.00 Amino acid : True - 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: 0.77 Conformation dependent library (CDL) restraints added in 398.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 11 sheets defined 56.9% alpha, 8.7% beta 21 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 38 through 41 Processing helix chain 'B' and resid 44 through 47 Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.630A pdb=" N PHE B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 4.608A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.607A pdb=" N MET B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.914A pdb=" N PHE B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.561A pdb=" N VAL B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.553A pdb=" N LEU B 213 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 4.004A pdb=" N GLU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.819A pdb=" N TYR B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.799A pdb=" N ILE A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 422 removed outlier: 4.625A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 441 removed outlier: 3.811A pdb=" N ALA A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 478 removed outlier: 3.525A pdb=" N TRP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Proline residue: A 463 - end of helix removed outlier: 3.637A pdb=" N GLU A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.643A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.898A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 removed outlier: 4.650A pdb=" N ARG A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 703 through 717 removed outlier: 4.131A pdb=" N VAL A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.913A pdb=" N GLY A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 813 removed outlier: 3.571A pdb=" N ALA A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 813 " --> pdb=" O ILE A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 857 through 873 removed outlier: 4.407A pdb=" N LEU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 890 through 900 removed outlier: 3.734A pdb=" N ASN A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 913 through 929 removed outlier: 4.335A pdb=" N ALA A 919 " --> pdb=" O TRP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 935 Processing helix chain 'A' and resid 948 through 959 removed outlier: 3.581A pdb=" N TYR A 954 " --> pdb=" O GLY A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 977 through 995 removed outlier: 3.997A pdb=" N HIS A 981 " --> pdb=" O ASP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 removed outlier: 4.023A pdb=" N ILE A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1019 removed outlier: 3.671A pdb=" N VAL A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 removed outlier: 3.643A pdb=" N SER A1038 " --> pdb=" O ALA A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1041 No H-bonds generated for 'chain 'A' and resid 1039 through 1041' Processing helix chain 'A' and resid 1048 through 1062 removed outlier: 3.639A pdb=" N LYS A1052 " --> pdb=" O LEU A1048 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1067 through 1085 removed outlier: 3.730A pdb=" N ILE A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1181 removed outlier: 3.916A pdb=" N LYS A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.768A pdb=" N ILE A1162 " --> pdb=" O PRO A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1214 Processing helix chain 'A' and resid 1217 through 1229 Processing helix chain 'A' and resid 1242 through 1255 removed outlier: 4.194A pdb=" N ILE A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A1255 " --> pdb=" O ILE A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.788A pdb=" N GLU A1272 " --> pdb=" O GLU A1268 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A1274 " --> pdb=" O TYR A1270 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A1275 " --> pdb=" O PHE A1271 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A1277 " --> pdb=" O LYS A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1292 removed outlier: 3.801A pdb=" N LYS A1292 " --> pdb=" O ASN A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1303 Processing helix chain 'A' and resid 1339 through 1346 removed outlier: 3.709A pdb=" N VAL A1342 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1343 " --> pdb=" O VAL A1340 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.466A pdb=" N TYR B 73 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU B 98 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B 75 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS B 49 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 10.997A pdb=" N LYS B 165 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE B 132 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS B 167 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 242 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE B 207 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 244 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ILE B 227 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE B 205 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 614 through 619 Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 684 removed outlier: 4.816A pdb=" N TRP A 682 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER A 687 " --> pdb=" O TRP A 682 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 818 through 819 removed outlier: 3.511A pdb=" N LEU A 818 " --> pdb=" O TRP A 734 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856 removed outlier: 3.679A pdb=" N LYS A 855 " --> pdb=" O SER A 938 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1185 through 1187 Processing sheet with id=AA9, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB2, first strand: chain 'A' and resid 1128 through 1131 502 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2700 1.33 - 1.45: 2486 1.45 - 1.57: 6236 1.57 - 1.69: 115 1.69 - 1.81: 59 Bond restraints: 11596 Sorted by residual: bond pdb=" C2' DT T 34 " pdb=" C1' DT T 34 " ideal model delta sigma weight residual 1.525 1.394 0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" O3' DG T 8 " pdb=" P DC T 9 " ideal model delta sigma weight residual 1.607 1.520 0.087 1.50e-02 4.44e+03 3.35e+01 bond pdb=" N ILE B 112 " pdb=" CA ILE B 112 " ideal model delta sigma weight residual 1.452 1.499 -0.047 1.18e-02 7.18e+03 1.57e+01 bond pdb=" C2' DA T 17 " pdb=" C1' DA T 17 " ideal model delta sigma weight residual 1.525 1.596 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N ILE A 665 " pdb=" CA ILE A 665 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.62e+00 ... (remaining 11591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 15809 3.19 - 6.38: 118 6.38 - 9.56: 15 9.56 - 12.75: 4 12.75 - 15.94: 1 Bond angle restraints: 15947 Sorted by residual: angle pdb=" O3' DT T 34 " pdb=" C3' DT T 34 " pdb=" C2' DT T 34 " ideal model delta sigma weight residual 111.50 101.12 10.38 1.50e+00 4.44e-01 4.78e+01 angle pdb=" O3' DT T 16 " pdb=" P DA T 17 " pdb=" OP2 DA T 17 " ideal model delta sigma weight residual 108.00 123.94 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" C3' DA T 17 " pdb=" O3' DA T 17 " pdb=" P DC T 18 " ideal model delta sigma weight residual 120.20 112.40 7.80 1.50e+00 4.44e-01 2.71e+01 angle pdb=" N ILE A 665 " pdb=" CA ILE A 665 " pdb=" C ILE A 665 " ideal model delta sigma weight residual 110.42 115.35 -4.93 9.60e-01 1.09e+00 2.63e+01 angle pdb=" C5' DA N 129 " pdb=" C4' DA N 129 " pdb=" O4' DA N 129 " ideal model delta sigma weight residual 109.40 117.01 -7.61 1.50e+00 4.44e-01 2.57e+01 ... (remaining 15942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 6539 34.84 - 69.69: 308 69.69 - 104.53: 10 104.53 - 139.37: 4 139.37 - 174.21: 4 Dihedral angle restraints: 6865 sinusoidal: 3191 harmonic: 3674 Sorted by residual: dihedral pdb=" O3B GTP A1402 " pdb=" O3A GTP A1402 " pdb=" PB GTP A1402 " pdb=" PA GTP A1402 " ideal model delta sinusoidal sigma weight residual 291.08 131.99 159.09 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O2G GTP A1402 " pdb=" O3B GTP A1402 " pdb=" PG GTP A1402 " pdb=" PB GTP A1402 " ideal model delta sinusoidal sigma weight residual 177.30 -25.73 -156.97 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' GTP A1402 " pdb=" O5' GTP A1402 " pdb=" PA GTP A1402 " pdb=" O3A GTP A1402 " ideal model delta sinusoidal sigma weight residual 69.27 -150.39 -140.34 1 2.00e+01 2.50e-03 4.25e+01 ... (remaining 6862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1715 0.117 - 0.235: 36 0.235 - 0.352: 4 0.352 - 0.469: 3 0.469 - 0.586: 1 Chirality restraints: 1759 Sorted by residual: chirality pdb=" C1' DT T 34 " pdb=" O4' DT T 34 " pdb=" C2' DT T 34 " pdb=" N1 DT T 34 " both_signs ideal model delta sigma weight residual False 2.47 1.88 0.59 2.00e-01 2.50e+01 8.59e+00 chirality pdb=" P DA T 17 " pdb=" OP1 DA T 17 " pdb=" OP2 DA T 17 " pdb=" O5' DA T 17 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" P DC T 18 " pdb=" OP1 DC T 18 " pdb=" OP2 DC T 18 " pdb=" O5' DC T 18 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.45 2.00e-01 2.50e+01 4.96e+00 ... (remaining 1756 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 932 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO A 933 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 933 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 933 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 852 " -0.014 2.00e-02 2.50e+03 1.66e-02 6.93e+00 pdb=" CG TRP A 852 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 852 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 852 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 852 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 852 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 852 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 852 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 852 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 852 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 668 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.27e+00 pdb=" C VAL A 668 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL A 668 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 669 " -0.013 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 89 2.60 - 3.17: 9040 3.17 - 3.75: 16783 3.75 - 4.32: 24053 4.32 - 4.90: 39590 Nonbonded interactions: 89555 Sorted by model distance: nonbonded pdb="MG MG A1401 " pdb=" O1B GTP A1402 " model vdw 2.023 2.170 nonbonded pdb=" OD1 ASP A 945 " pdb="MG MG A1401 " model vdw 2.025 2.170 nonbonded pdb=" OD2 ASP A1189 " pdb="MG MG A1401 " model vdw 2.107 2.170 nonbonded pdb="MG MG A1401 " pdb=" O2G GTP A1402 " model vdw 2.111 2.170 nonbonded pdb=" O GLY A 946 " pdb="MG MG A1401 " model vdw 2.122 2.170 ... (remaining 89550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.005 0.131 11596 Z= 0.269 Angle : 0.762 15.941 15947 Z= 0.438 Chirality : 0.053 0.586 1759 Planarity : 0.005 0.070 1835 Dihedral : 18.362 174.214 4483 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.27 % Allowed : 1.10 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.24), residues: 1247 helix: 0.95 (0.21), residues: 633 sheet: -0.19 (0.57), residues: 97 loop : -0.82 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 100 TYR 0.022 0.002 TYR A 805 PHE 0.016 0.001 PHE B 331 TRP 0.041 0.002 TRP A 852 HIS 0.004 0.001 HIS A 953 Details of bonding type rmsd covalent geometry : bond 0.00499 (11596) covalent geometry : angle 0.76238 (15947) hydrogen bonds : bond 0.19562 ( 549) hydrogen bonds : angle 6.36007 ( 1513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7774 (mttt) cc_final: 0.7424 (pttm) outliers start: 3 outliers final: 1 residues processed: 134 average time/residue: 0.1204 time to fit residues: 22.4891 Evaluate side-chains 105 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 GLN A1070 HIS A1129 GLN A1169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.149607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.123924 restraints weight = 13974.608| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.40 r_work: 0.3052 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11596 Z= 0.293 Angle : 0.684 7.053 15947 Z= 0.368 Chirality : 0.045 0.171 1759 Planarity : 0.005 0.049 1835 Dihedral : 20.112 173.713 2002 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.00 % Allowed : 9.22 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.24), residues: 1247 helix: 0.90 (0.21), residues: 647 sheet: -0.02 (0.55), residues: 107 loop : -0.98 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 116 TYR 0.018 0.002 TYR A 805 PHE 0.018 0.002 PHE A 546 TRP 0.023 0.002 TRP A 852 HIS 0.006 0.002 HIS A1188 Details of bonding type rmsd covalent geometry : bond 0.00703 (11596) covalent geometry : angle 0.68450 (15947) hydrogen bonds : bond 0.07071 ( 549) hydrogen bonds : angle 4.67612 ( 1513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8086 (mttt) cc_final: 0.7404 (pttm) REVERT: B 168 MET cc_start: 0.8816 (ttp) cc_final: 0.8528 (ttm) REVERT: B 251 ASP cc_start: 0.7997 (p0) cc_final: 0.7585 (p0) REVERT: B 310 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 893 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7336 (t0) outliers start: 11 outliers final: 9 residues processed: 119 average time/residue: 0.1225 time to fit residues: 20.2135 Evaluate side-chains 111 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.162927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.139855 restraints weight = 13779.472| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.17 r_work: 0.3127 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11596 Z= 0.159 Angle : 0.559 9.939 15947 Z= 0.299 Chirality : 0.040 0.161 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.810 177.267 2002 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.19 % Allowed : 12.33 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1247 helix: 1.32 (0.21), residues: 640 sheet: 0.17 (0.56), residues: 108 loop : -0.96 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.014 0.001 TYR B 161 PHE 0.016 0.001 PHE A 826 TRP 0.017 0.002 TRP A 852 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00372 (11596) covalent geometry : angle 0.55859 (15947) hydrogen bonds : bond 0.05242 ( 549) hydrogen bonds : angle 4.20856 ( 1513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8044 (mttt) cc_final: 0.7369 (pttm) REVERT: B 60 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: B 168 MET cc_start: 0.8713 (ttp) cc_final: 0.8457 (ttm) REVERT: A 433 HIS cc_start: 0.7371 (t-170) cc_final: 0.7087 (t-170) REVERT: A 893 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7235 (t0) outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.1083 time to fit residues: 18.9127 Evaluate side-chains 115 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1087 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.149081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123916 restraints weight = 13972.348| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.34 r_work: 0.3052 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11596 Z= 0.268 Angle : 0.657 10.008 15947 Z= 0.349 Chirality : 0.044 0.189 1759 Planarity : 0.005 0.048 1835 Dihedral : 20.005 174.973 2002 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.56 % Allowed : 14.06 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.24), residues: 1247 helix: 0.97 (0.21), residues: 648 sheet: 0.23 (0.56), residues: 107 loop : -1.04 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 883 TYR 0.020 0.002 TYR A 805 PHE 0.017 0.002 PHE A 886 TRP 0.023 0.002 TRP B 235 HIS 0.005 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00650 (11596) covalent geometry : angle 0.65659 (15947) hydrogen bonds : bond 0.06398 ( 549) hydrogen bonds : angle 4.43612 ( 1513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8063 (mttt) cc_final: 0.7442 (ttpt) REVERT: B 60 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: B 168 MET cc_start: 0.8827 (ttp) cc_final: 0.8587 (ttm) REVERT: B 251 ASP cc_start: 0.8009 (p0) cc_final: 0.7696 (p0) REVERT: B 310 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: A 893 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7187 (t0) outliers start: 28 outliers final: 21 residues processed: 131 average time/residue: 0.1065 time to fit residues: 19.8051 Evaluate side-chains 124 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.152741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.124856 restraints weight = 13813.699| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.38 r_work: 0.3118 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11596 Z= 0.138 Angle : 0.538 9.635 15947 Z= 0.289 Chirality : 0.039 0.159 1759 Planarity : 0.004 0.048 1835 Dihedral : 19.737 178.051 2002 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.37 % Allowed : 14.43 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.25), residues: 1247 helix: 1.47 (0.21), residues: 637 sheet: 0.30 (0.56), residues: 108 loop : -0.95 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.014 0.001 TYR B 161 PHE 0.015 0.001 PHE A 826 TRP 0.013 0.001 TRP A 852 HIS 0.004 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00319 (11596) covalent geometry : angle 0.53751 (15947) hydrogen bonds : bond 0.04848 ( 549) hydrogen bonds : angle 4.04432 ( 1513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8007 (mttt) cc_final: 0.7324 (pttm) REVERT: B 60 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: B 100 ARG cc_start: 0.7688 (mtt90) cc_final: 0.7227 (mtp180) REVERT: B 168 MET cc_start: 0.8746 (ttp) cc_final: 0.8523 (ttm) REVERT: B 251 ASP cc_start: 0.8113 (p0) cc_final: 0.7741 (p0) REVERT: A 893 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7116 (t0) REVERT: A 926 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: A 1212 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8224 (tp) outliers start: 26 outliers final: 15 residues processed: 138 average time/residue: 0.1105 time to fit residues: 21.5984 Evaluate side-chains 122 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.160016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.135931 restraints weight = 13914.768| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.22 r_work: 0.3087 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11596 Z= 0.219 Angle : 0.600 8.957 15947 Z= 0.320 Chirality : 0.042 0.170 1759 Planarity : 0.005 0.048 1835 Dihedral : 19.784 175.130 2002 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.83 % Allowed : 14.61 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.25), residues: 1247 helix: 1.25 (0.21), residues: 647 sheet: 0.45 (0.57), residues: 105 loop : -1.05 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 883 TYR 0.015 0.002 TYR A 805 PHE 0.016 0.002 PHE A 886 TRP 0.013 0.002 TRP A 592 HIS 0.005 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00526 (11596) covalent geometry : angle 0.60010 (15947) hydrogen bonds : bond 0.05686 ( 549) hydrogen bonds : angle 4.20562 ( 1513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8056 (mttt) cc_final: 0.7444 (ttpt) REVERT: B 60 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: B 100 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7256 (mtp180) REVERT: B 114 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6869 (tt0) REVERT: B 168 MET cc_start: 0.8794 (ttp) cc_final: 0.8566 (ttm) REVERT: B 251 ASP cc_start: 0.8102 (p0) cc_final: 0.7716 (p0) REVERT: A 893 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7156 (t0) REVERT: A 926 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: A 1212 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8282 (tp) outliers start: 31 outliers final: 26 residues processed: 132 average time/residue: 0.1008 time to fit residues: 19.0908 Evaluate side-chains 132 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1020 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.159230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.135481 restraints weight = 13751.391| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.18 r_work: 0.3096 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11596 Z= 0.206 Angle : 0.592 8.778 15947 Z= 0.317 Chirality : 0.041 0.160 1759 Planarity : 0.004 0.048 1835 Dihedral : 19.753 175.075 2002 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.11 % Allowed : 15.16 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.25), residues: 1247 helix: 1.23 (0.21), residues: 648 sheet: 0.38 (0.56), residues: 105 loop : -1.03 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 883 TYR 0.014 0.002 TYR B 42 PHE 0.016 0.002 PHE A 826 TRP 0.015 0.002 TRP A 592 HIS 0.005 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00495 (11596) covalent geometry : angle 0.59214 (15947) hydrogen bonds : bond 0.05553 ( 549) hydrogen bonds : angle 4.19167 ( 1513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8076 (mttt) cc_final: 0.7452 (ttpt) REVERT: B 60 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: B 100 ARG cc_start: 0.7753 (mtt90) cc_final: 0.7250 (mtp180) REVERT: B 168 MET cc_start: 0.8780 (ttp) cc_final: 0.8567 (ttm) REVERT: B 214 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7527 (ttpt) REVERT: B 251 ASP cc_start: 0.8108 (p0) cc_final: 0.7735 (p0) REVERT: A 893 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7163 (t0) REVERT: A 926 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: A 1197 ASP cc_start: 0.8086 (m-30) cc_final: 0.7827 (m-30) REVERT: A 1212 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8282 (tp) outliers start: 34 outliers final: 29 residues processed: 133 average time/residue: 0.1047 time to fit residues: 20.0744 Evaluate side-chains 135 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1020 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN A1208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.164765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.141312 restraints weight = 13720.178| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.21 r_work: 0.3157 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11596 Z= 0.122 Angle : 0.515 8.895 15947 Z= 0.277 Chirality : 0.038 0.153 1759 Planarity : 0.004 0.048 1835 Dihedral : 19.518 176.356 2002 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.01 % Allowed : 16.71 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1247 helix: 1.73 (0.21), residues: 633 sheet: 0.38 (0.57), residues: 108 loop : -0.84 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 800 TYR 0.014 0.001 TYR B 161 PHE 0.014 0.001 PHE A 826 TRP 0.015 0.001 TRP A 852 HIS 0.006 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00276 (11596) covalent geometry : angle 0.51450 (15947) hydrogen bonds : bond 0.04272 ( 549) hydrogen bonds : angle 3.87560 ( 1513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7971 (mttt) cc_final: 0.7427 (ttpt) REVERT: B 60 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: B 100 ARG cc_start: 0.7738 (mtt90) cc_final: 0.7260 (mtp180) REVERT: B 114 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6844 (tt0) REVERT: B 168 MET cc_start: 0.8719 (ttp) cc_final: 0.8508 (ttm) REVERT: B 251 ASP cc_start: 0.8014 (p0) cc_final: 0.7735 (p0) REVERT: A 926 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: A 1197 ASP cc_start: 0.8101 (m-30) cc_final: 0.7861 (m-30) REVERT: A 1212 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8169 (tp) outliers start: 22 outliers final: 17 residues processed: 128 average time/residue: 0.1125 time to fit residues: 20.3492 Evaluate side-chains 122 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.158443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.133664 restraints weight = 13681.767| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.25 r_work: 0.3093 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11596 Z= 0.214 Angle : 0.593 9.040 15947 Z= 0.316 Chirality : 0.042 0.176 1759 Planarity : 0.004 0.046 1835 Dihedral : 19.684 174.503 2002 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.56 % Allowed : 16.62 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.25), residues: 1247 helix: 1.34 (0.21), residues: 647 sheet: 0.26 (0.56), residues: 108 loop : -0.95 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 100 TYR 0.013 0.002 TYR A 805 PHE 0.016 0.002 PHE A 886 TRP 0.012 0.002 TRP A 592 HIS 0.005 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00511 (11596) covalent geometry : angle 0.59347 (15947) hydrogen bonds : bond 0.05421 ( 549) hydrogen bonds : angle 4.12083 ( 1513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8069 (mttt) cc_final: 0.7453 (ttpt) REVERT: B 60 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: B 100 ARG cc_start: 0.7789 (mtt90) cc_final: 0.7284 (mtp180) REVERT: B 114 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6943 (tt0) REVERT: B 168 MET cc_start: 0.8799 (ttp) cc_final: 0.8589 (ttm) REVERT: B 251 ASP cc_start: 0.8053 (p0) cc_final: 0.7773 (p0) REVERT: A 893 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7192 (t0) REVERT: A 926 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: A 996 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6829 (ptmt) REVERT: A 1197 ASP cc_start: 0.8183 (m-30) cc_final: 0.7955 (m-30) REVERT: A 1212 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8282 (tp) outliers start: 28 outliers final: 23 residues processed: 125 average time/residue: 0.1208 time to fit residues: 21.3234 Evaluate side-chains 129 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.155730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.130833 restraints weight = 13811.955| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.31 r_work: 0.3108 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11596 Z= 0.227 Angle : 0.616 8.990 15947 Z= 0.329 Chirality : 0.043 0.185 1759 Planarity : 0.005 0.048 1835 Dihedral : 19.790 174.136 2002 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.56 % Allowed : 16.71 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.24), residues: 1247 helix: 1.10 (0.21), residues: 653 sheet: 0.34 (0.56), residues: 105 loop : -1.02 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 686 TYR 0.015 0.002 TYR A 805 PHE 0.017 0.002 PHE A 886 TRP 0.016 0.002 TRP A 592 HIS 0.006 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00547 (11596) covalent geometry : angle 0.61650 (15947) hydrogen bonds : bond 0.05770 ( 549) hydrogen bonds : angle 4.26171 ( 1513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8041 (mttt) cc_final: 0.7460 (ttpt) REVERT: B 60 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: B 100 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7307 (mtp180) REVERT: B 114 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6984 (tt0) REVERT: B 168 MET cc_start: 0.8766 (ttp) cc_final: 0.8557 (ttm) REVERT: B 251 ASP cc_start: 0.8040 (p0) cc_final: 0.7764 (p0) REVERT: A 686 ARG cc_start: 0.7607 (ptm160) cc_final: 0.7219 (ptp90) REVERT: A 893 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7222 (t0) REVERT: A 926 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 1197 ASP cc_start: 0.8134 (m-30) cc_final: 0.7922 (m-30) REVERT: A 1212 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8307 (tp) outliers start: 28 outliers final: 23 residues processed: 123 average time/residue: 0.1143 time to fit residues: 20.0519 Evaluate side-chains 128 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.162571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.138754 restraints weight = 13742.807| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.21 r_work: 0.3114 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11596 Z= 0.149 Angle : 0.551 8.955 15947 Z= 0.295 Chirality : 0.039 0.158 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.654 175.326 2002 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 16.89 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1247 helix: 1.40 (0.21), residues: 651 sheet: 0.27 (0.56), residues: 108 loop : -0.90 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 686 TYR 0.013 0.001 TYR B 161 PHE 0.015 0.001 PHE A 826 TRP 0.015 0.002 TRP A 852 HIS 0.006 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00349 (11596) covalent geometry : angle 0.55145 (15947) hydrogen bonds : bond 0.04795 ( 549) hydrogen bonds : angle 4.01770 ( 1513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.07 seconds wall clock time: 35 minutes 47.34 seconds (2147.34 seconds total)