Starting phenix.real_space_refine on Sun Dec 29 17:10:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ap1_15556/12_2024/8ap1_15556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ap1_15556/12_2024/8ap1_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_15556/12_2024/8ap1_15556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ap1_15556/12_2024/8ap1_15556.map" model { file = "/net/cci-nas-00/data/ceres_data/8ap1_15556/12_2024/8ap1_15556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ap1_15556/12_2024/8ap1_15556.cif" } resolution = 3.47 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= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} 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:plan2': 1, ' DC:plan': 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: 6.18, per 1000 atoms: 0.55 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: 3.15 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.19 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: 4.86 Time building geometry restraints manager: 3.38 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: 0.200 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.930 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- 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= 0.299 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 (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: 0.17 (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 TRP 0.041 0.002 TRP A 852 HIS 0.004 0.001 HIS A 953 PHE 0.016 0.001 PHE B 331 TYR 0.022 0.002 TYR A 805 ARG 0.003 0.000 ARG B 100 *********************** 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 : 1.173 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: 0.2829 time to fit residues: 52.7379 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 : 1.082 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 0.0470 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11596 Z= 0.273 Angle : 0.587 7.063 15947 Z= 0.318 Chirality : 0.041 0.170 1759 Planarity : 0.005 0.049 1835 Dihedral : 19.870 174.581 2002 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.55 % Allowed : 7.85 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1247 helix: 1.37 (0.21), residues: 632 sheet: 0.06 (0.55), residues: 107 loop : -0.88 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 852 HIS 0.004 0.001 HIS A1188 PHE 0.016 0.002 PHE A 546 TYR 0.012 0.002 TYR A 805 ARG 0.003 0.000 ARG B 116 *********************** 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 122 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7926 (mttt) cc_final: 0.7460 (pttm) REVERT: B 168 MET cc_start: 0.8302 (ttp) cc_final: 0.8073 (ttm) outliers start: 6 outliers final: 5 residues processed: 120 average time/residue: 0.2823 time to fit residues: 47.7797 Evaluate side-chains 111 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 A 669 GLN A1208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11596 Z= 0.219 Angle : 0.537 6.786 15947 Z= 0.288 Chirality : 0.039 0.160 1759 Planarity : 0.004 0.046 1835 Dihedral : 19.685 177.699 2002 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.10 % Allowed : 10.96 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1247 helix: 1.57 (0.21), residues: 637 sheet: 0.20 (0.56), residues: 108 loop : -0.91 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 852 HIS 0.003 0.001 HIS A1188 PHE 0.014 0.001 PHE A 826 TYR 0.012 0.001 TYR B 161 ARG 0.002 0.000 ARG A 547 *********************** 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 133 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7969 (mttt) cc_final: 0.7460 (pttm) REVERT: B 60 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: B 168 MET cc_start: 0.8284 (ttp) cc_final: 0.8069 (ttm) REVERT: A 996 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6804 (ptmt) outliers start: 12 outliers final: 7 residues processed: 129 average time/residue: 0.2710 time to fit residues: 49.3854 Evaluate side-chains 115 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 GLN 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 795 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 96 GLN B 290 ASN A1169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1494 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= 0.345 Angle : 0.612 10.333 15947 Z= 0.326 Chirality : 0.042 0.174 1759 Planarity : 0.005 0.047 1835 Dihedral : 19.785 175.465 2002 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.83 % Allowed : 13.79 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1247 helix: 1.22 (0.21), residues: 648 sheet: 0.29 (0.56), residues: 107 loop : -0.96 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 235 HIS 0.004 0.001 HIS B 265 PHE 0.016 0.002 PHE A 886 TYR 0.017 0.002 TYR A 805 ARG 0.002 0.000 ARG A 663 *********************** 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 126 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8077 (mttt) cc_final: 0.7575 (ttpt) REVERT: B 60 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: B 168 MET cc_start: 0.8360 (ttp) cc_final: 0.8157 (ttm) REVERT: A 433 HIS cc_start: 0.7232 (t-170) cc_final: 0.6979 (t-170) outliers start: 20 outliers final: 15 residues processed: 120 average time/residue: 0.2672 time to fit residues: 45.2056 Evaluate side-chains 117 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 107 THR 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 596 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1025 THR 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 103 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11596 Z= 0.281 Angle : 0.569 10.418 15947 Z= 0.304 Chirality : 0.040 0.163 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.672 176.025 2002 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.56 % Allowed : 14.25 % 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 (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: 0.51 (0.25), residues: 1247 helix: 1.28 (0.21), residues: 651 sheet: 0.32 (0.57), residues: 107 loop : -0.92 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 235 HIS 0.004 0.001 HIS B 265 PHE 0.015 0.002 PHE A 826 TYR 0.014 0.002 TYR B 108 ARG 0.002 0.000 ARG A 883 *********************** 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 139 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8028 (mttt) cc_final: 0.7544 (ttpt) REVERT: B 60 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: A 926 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7201 (mp0) outliers start: 28 outliers final: 19 residues processed: 132 average time/residue: 0.2633 time to fit residues: 50.3410 Evaluate side-chains 124 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 522 THR 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 878 LEU 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 1027 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 40.0000 chunk 111 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11596 Z= 0.227 Angle : 0.539 9.844 15947 Z= 0.289 Chirality : 0.039 0.156 1759 Planarity : 0.004 0.046 1835 Dihedral : 19.581 176.105 2002 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.92 % Allowed : 15.25 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1247 helix: 1.48 (0.21), residues: 646 sheet: 0.36 (0.57), residues: 108 loop : -0.90 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 592 HIS 0.005 0.001 HIS A 433 PHE 0.014 0.001 PHE A 826 TYR 0.013 0.001 TYR B 161 ARG 0.002 0.000 ARG A 883 *********************** 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 133 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8008 (mttt) cc_final: 0.7572 (ttpt) REVERT: B 251 ASP cc_start: 0.7586 (p0) cc_final: 0.7283 (p0) REVERT: A 926 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: A 1197 ASP cc_start: 0.7813 (m-30) cc_final: 0.7581 (m-30) REVERT: A 1212 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8138 (tp) outliers start: 21 outliers final: 17 residues processed: 126 average time/residue: 0.2774 time to fit residues: 49.5570 Evaluate side-chains 123 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR 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 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 795 SER Chi-restraints excluded: chain A residue 878 LEU 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 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 119 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1690 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= 0.333 Angle : 0.596 9.392 15947 Z= 0.317 Chirality : 0.042 0.170 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.676 174.759 2002 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.56 % Allowed : 14.89 % 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 (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: 0.47 (0.25), residues: 1247 helix: 1.24 (0.21), residues: 652 sheet: 0.46 (0.57), residues: 105 loop : -0.98 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 592 HIS 0.005 0.001 HIS A 433 PHE 0.016 0.002 PHE A 886 TYR 0.015 0.002 TYR A 805 ARG 0.002 0.000 ARG A 883 *********************** 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 136 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8049 (mttt) cc_final: 0.7575 (ttpt) REVERT: B 60 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: B 251 ASP cc_start: 0.7627 (p0) cc_final: 0.7289 (p0) REVERT: A 926 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: A 1197 ASP cc_start: 0.7879 (m-30) cc_final: 0.7673 (m-30) REVERT: A 1212 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8202 (tp) outliers start: 28 outliers final: 24 residues processed: 128 average time/residue: 0.2566 time to fit residues: 47.0671 Evaluate side-chains 132 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 878 LEU 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 1027 VAL 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 49 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1718 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= 0.243 Angle : 0.549 9.258 15947 Z= 0.294 Chirality : 0.039 0.156 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.597 175.516 2002 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.37 % Allowed : 15.43 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1247 helix: 1.38 (0.21), residues: 650 sheet: 0.30 (0.57), residues: 108 loop : -0.90 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 592 HIS 0.006 0.001 HIS A 433 PHE 0.015 0.001 PHE A 826 TYR 0.020 0.001 TYR B 108 ARG 0.002 0.000 ARG A 883 *********************** 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 133 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8048 (mttt) cc_final: 0.7606 (ttpt) REVERT: B 60 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: B 251 ASP cc_start: 0.7551 (p0) cc_final: 0.7326 (p0) REVERT: A 926 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: A 1212 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8159 (tp) outliers start: 26 outliers final: 23 residues processed: 127 average time/residue: 0.2530 time to fit residues: 46.0784 Evaluate side-chains 129 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1027 VAL 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 118 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1748 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= 0.315 Angle : 0.588 9.352 15947 Z= 0.314 Chirality : 0.041 0.194 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.671 174.621 2002 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.65 % Allowed : 15.53 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1247 helix: 1.23 (0.21), residues: 652 sheet: 0.40 (0.57), residues: 105 loop : -0.97 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 592 HIS 0.006 0.001 HIS A 433 PHE 0.015 0.002 PHE A 886 TYR 0.022 0.002 TYR B 108 ARG 0.002 0.000 ARG A 883 *********************** 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 133 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8060 (mttt) cc_final: 0.7603 (ttpt) REVERT: B 60 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: B 251 ASP cc_start: 0.7606 (p0) cc_final: 0.7265 (p0) REVERT: A 926 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: A 1197 ASP cc_start: 0.7910 (m-30) cc_final: 0.7622 (m-30) REVERT: A 1212 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8196 (tp) outliers start: 29 outliers final: 24 residues processed: 125 average time/residue: 0.2463 time to fit residues: 43.9395 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 : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 1027 VAL 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: 5.9990 chunk 57 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 40.0000 chunk 101 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 108 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1769 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= 0.316 Angle : 0.594 9.314 15947 Z= 0.317 Chirality : 0.042 0.189 1759 Planarity : 0.004 0.048 1835 Dihedral : 19.683 174.592 2002 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.74 % Allowed : 15.62 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1247 helix: 1.18 (0.21), residues: 653 sheet: 0.42 (0.57), residues: 105 loop : -0.97 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 592 HIS 0.006 0.001 HIS A 433 PHE 0.015 0.002 PHE A 886 TYR 0.021 0.002 TYR B 108 ARG 0.002 0.000 ARG A 883 ********************** 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 134 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8045 (mttt) cc_final: 0.7599 (ttpt) REVERT: B 60 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: B 251 ASP cc_start: 0.7604 (p0) cc_final: 0.7269 (p0) REVERT: A 926 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: A 1197 ASP cc_start: 0.7886 (m-30) cc_final: 0.7596 (m-30) REVERT: A 1212 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8199 (tp) outliers start: 30 outliers final: 24 residues processed: 126 average time/residue: 0.2493 time to fit residues: 45.2207 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 : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 596 ILE 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 926 GLU Chi-restraints excluded: chain A residue 1018 MET 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 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 31 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.153534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.128631 restraints weight = 13781.706| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.26 r_work: 0.3146 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1818 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= 0.205 Angle : 0.533 9.299 15947 Z= 0.286 Chirality : 0.039 0.157 1759 Planarity : 0.004 0.048 1835 Dihedral : 19.546 175.598 2002 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.37 % Allowed : 16.07 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1247 helix: 1.49 (0.21), residues: 651 sheet: 0.40 (0.57), residues: 108 loop : -0.84 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 852 HIS 0.006 0.001 HIS A 433 PHE 0.015 0.001 PHE A 826 TYR 0.013 0.001 TYR B 161 ARG 0.001 0.000 ARG A 686 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.69 seconds wall clock time: 38 minutes 22.92 seconds (2302.92 seconds total)