Starting phenix.real_space_refine on Tue Jul 29 04:24:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ap1_15556/07_2025/8ap1_15556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ap1_15556/07_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_15556/07_2025/8ap1_15556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ap1_15556/07_2025/8ap1_15556.map" model { file = "/net/cci-nas-00/data/ceres_data/8ap1_15556/07_2025/8ap1_15556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ap1_15556/07_2025/8ap1_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-5711/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: 6.98, per 1000 atoms: 0.62 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: 3.41 Conformation dependent library (CDL) restraints added in 2.8 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: 4.33 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: 7.32 Time building geometry restraints manager: 3.80 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: 0.350 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 39.240 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 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:4.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.19562 ( 549) hydrogen bonds : angle 6.36007 ( 1513) covalent geometry : bond 0.00499 (11596) covalent geometry : angle 0.76238 (15947) *********************** 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 : 2.979 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: 0.3267 time to fit residues: 62.6327 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 : 1.672 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.161472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.137377 restraints weight = 13673.409| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.29 r_work: 0.3112 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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= 0.188 Angle : 0.587 7.063 15947 Z= 0.318 Chirality : 0.041 0.169 1759 Planarity : 0.005 0.049 1835 Dihedral : 19.870 174.580 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 Details of bonding type rmsd hydrogen bonds : bond 0.06096 ( 549) hydrogen bonds : angle 4.43621 ( 1513) covalent geometry : bond 0.00432 (11596) covalent geometry : angle 0.58687 (15947) *********************** 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 : 1.206 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7988 (mttt) cc_final: 0.7354 (pttm) REVERT: B 168 MET cc_start: 0.8716 (ttp) cc_final: 0.8437 (ttm) outliers start: 6 outliers final: 5 residues processed: 120 average time/residue: 0.2777 time to fit residues: 46.6397 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 : 1.178 ------------------------------------------------------------------------------- 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 82 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 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 30 ASN A 669 GLN A1169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.150601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.124412 restraints weight = 13952.277| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.42 r_work: 0.3059 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11596 Z= 0.232 Angle : 0.620 6.821 15947 Z= 0.332 Chirality : 0.043 0.198 1759 Planarity : 0.005 0.046 1835 Dihedral : 19.968 176.360 2002 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.55 % Allowed : 11.42 % Favored : 87.03 % 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: 0.33 (0.25), residues: 1247 helix: 1.15 (0.21), residues: 646 sheet: 0.17 (0.56), residues: 107 loop : -0.98 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 235 HIS 0.005 0.001 HIS A1188 PHE 0.015 0.002 PHE A 826 TYR 0.018 0.002 TYR A 805 ARG 0.002 0.000 ARG A 663 Details of bonding type rmsd hydrogen bonds : bond 0.06176 ( 549) hydrogen bonds : angle 4.38352 ( 1513) covalent geometry : bond 0.00560 (11596) covalent geometry : angle 0.61995 (15947) *********************** 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 127 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8077 (mttt) cc_final: 0.7432 (ttpt) REVERT: B 60 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: B 168 MET cc_start: 0.8828 (ttp) cc_final: 0.8563 (ttm) REVERT: B 251 ASP cc_start: 0.7976 (p0) cc_final: 0.7592 (p0) REVERT: A 433 HIS cc_start: 0.7369 (t-170) cc_final: 0.7034 (t-170) REVERT: A 893 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7325 (t0) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 0.2601 time to fit residues: 45.3734 Evaluate side-chains 116 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 200 THR Chi-restraints excluded: chain B residue 207 ILE 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 596 ILE Chi-restraints excluded: chain A residue 602 SER 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 893 ASP 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 43 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.163719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.140458 restraints weight = 13686.963| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.18 r_work: 0.3135 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1435 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= 0.159 Angle : 0.550 9.331 15947 Z= 0.294 Chirality : 0.039 0.159 1759 Planarity : 0.004 0.046 1835 Dihedral : 19.712 176.446 2002 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.28 % Allowed : 13.33 % Favored : 85.39 % 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: 0.59 (0.25), residues: 1247 helix: 1.42 (0.21), residues: 643 sheet: 0.24 (0.56), residues: 108 loop : -0.93 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 852 HIS 0.003 0.001 HIS B 265 PHE 0.015 0.001 PHE A 826 TYR 0.013 0.001 TYR B 161 ARG 0.002 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.05091 ( 549) hydrogen bonds : angle 4.09676 ( 1513) covalent geometry : bond 0.00374 (11596) covalent geometry : angle 0.54990 (15947) *********************** 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 134 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8013 (mttt) cc_final: 0.7321 (pttm) REVERT: B 100 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7330 (mtp180) REVERT: B 168 MET cc_start: 0.8925 (ttp) cc_final: 0.8675 (ttm) REVERT: A 433 HIS cc_start: 0.7426 (t-170) cc_final: 0.7104 (t-170) REVERT: A 893 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7250 (t0) outliers start: 14 outliers final: 10 residues processed: 129 average time/residue: 0.3438 time to fit residues: 64.7965 Evaluate side-chains 117 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 596 ILE 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 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 106 optimal weight: 3.9990 chunk 41 optimal weight: 40.0000 chunk 126 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 9 optimal weight: 0.0030 chunk 36 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 290 ASN A 684 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.162835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.139493 restraints weight = 13700.637| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.19 r_work: 0.3128 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1547 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= 0.153 Angle : 0.539 10.264 15947 Z= 0.288 Chirality : 0.039 0.157 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.626 176.410 2002 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.47 % Allowed : 14.06 % Favored : 83.47 % 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: 1.55 (0.21), residues: 643 sheet: 0.31 (0.57), residues: 108 loop : -0.92 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 864 HIS 0.003 0.001 HIS B 265 PHE 0.014 0.001 PHE A 826 TYR 0.012 0.001 TYR B 161 ARG 0.002 0.000 ARG A 883 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 549) hydrogen bonds : angle 3.99180 ( 1513) covalent geometry : bond 0.00361 (11596) covalent geometry : angle 0.53890 (15947) *********************** 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: 27 poor density : 117 time to evaluate : 1.569 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8018 (mttt) cc_final: 0.7433 (ttpt) REVERT: B 60 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: B 100 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7266 (mtp180) REVERT: B 114 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6779 (tt0) REVERT: B 168 MET cc_start: 0.8750 (ttp) cc_final: 0.8517 (ttm) REVERT: A 433 HIS cc_start: 0.7394 (t-170) cc_final: 0.7082 (t-170) REVERT: A 893 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7069 (t0) REVERT: A 926 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7321 (mp0) outliers start: 27 outliers final: 18 residues processed: 137 average time/residue: 0.2777 time to fit residues: 54.0682 Evaluate side-chains 129 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 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 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 696 THR 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 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 1233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 77 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 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 = 0.3706 r_free = 0.3706 target = 0.160965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.136805 restraints weight = 13829.659| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.22 r_work: 0.3098 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11596 Z= 0.201 Angle : 0.584 10.394 15947 Z= 0.311 Chirality : 0.041 0.165 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.673 175.200 2002 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.65 % Allowed : 14.16 % 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: 0.55 (0.25), residues: 1247 helix: 1.32 (0.21), residues: 651 sheet: 0.33 (0.57), residues: 107 loop : -0.91 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 592 HIS 0.004 0.001 HIS B 265 PHE 0.015 0.002 PHE A 886 TYR 0.014 0.002 TYR A 805 ARG 0.002 0.000 ARG A 883 Details of bonding type rmsd hydrogen bonds : bond 0.05437 ( 549) hydrogen bonds : angle 4.11337 ( 1513) covalent geometry : bond 0.00483 (11596) covalent geometry : angle 0.58414 (15947) *********************** 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: 29 poor density : 110 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8037 (mttt) cc_final: 0.7424 (ttpt) REVERT: B 60 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: B 100 ARG cc_start: 0.7757 (mtt90) cc_final: 0.7272 (mtp180) REVERT: B 114 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6820 (tt0) REVERT: B 168 MET cc_start: 0.8785 (ttp) cc_final: 0.8549 (ttm) REVERT: B 251 ASP cc_start: 0.8002 (p0) cc_final: 0.7727 (p0) REVERT: A 433 HIS cc_start: 0.7372 (t-170) cc_final: 0.7116 (t-170) REVERT: A 893 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7170 (t0) REVERT: A 926 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 1212 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8280 (tp) outliers start: 29 outliers final: 22 residues processed: 133 average time/residue: 0.2412 time to fit residues: 46.3302 Evaluate side-chains 131 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 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 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 1027 VAL 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 122 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.153454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.127656 restraints weight = 14012.969| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.33 r_work: 0.3103 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.003 0.039 11596 Z= 0.138 Angle : 0.528 10.009 15947 Z= 0.283 Chirality : 0.039 0.155 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.551 175.984 2002 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 0.77 (0.25), residues: 1247 helix: 1.58 (0.21), residues: 644 sheet: 0.38 (0.57), residues: 108 loop : -0.88 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 592 HIS 0.003 0.001 HIS B 265 PHE 0.014 0.001 PHE A 826 TYR 0.013 0.001 TYR B 161 ARG 0.002 0.000 ARG B 100 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 549) hydrogen bonds : angle 3.93620 ( 1513) covalent geometry : bond 0.00321 (11596) covalent geometry : angle 0.52803 (15947) *********************** 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 131 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7965 (mttt) cc_final: 0.7405 (ttpt) REVERT: B 60 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: B 100 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7278 (mtp180) REVERT: B 168 MET cc_start: 0.8806 (ttp) cc_final: 0.8574 (ttm) REVERT: B 251 ASP cc_start: 0.8125 (p0) cc_final: 0.7915 (p0) REVERT: A 433 HIS cc_start: 0.7388 (t-170) cc_final: 0.7157 (t-170) REVERT: A 893 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7140 (t0) REVERT: A 926 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: A 1212 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8232 (tp) outliers start: 21 outliers final: 17 residues processed: 125 average time/residue: 0.2799 time to fit residues: 50.5400 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 : 1.301 ------------------------------------------------------------------------------- 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 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 795 SER 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 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 70 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.153486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.128487 restraints weight = 13881.087| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.29 r_work: 0.3120 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11596 Z= 0.141 Angle : 0.528 9.678 15947 Z= 0.282 Chirality : 0.039 0.174 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.517 175.796 2002 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.74 % Allowed : 14.89 % Favored : 82.37 % 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: 0.81 (0.25), residues: 1247 helix: 1.59 (0.21), residues: 647 sheet: 0.42 (0.56), residues: 108 loop : -0.87 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 592 HIS 0.003 0.001 HIS B 265 PHE 0.014 0.001 PHE A 826 TYR 0.012 0.001 TYR B 161 ARG 0.002 0.000 ARG B 100 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 549) hydrogen bonds : angle 3.90406 ( 1513) covalent geometry : bond 0.00329 (11596) covalent geometry : angle 0.52848 (15947) *********************** 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 136 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7984 (mttt) cc_final: 0.7437 (ttpt) REVERT: B 60 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: B 100 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7248 (mtp180) REVERT: B 114 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6888 (tt0) REVERT: B 168 MET cc_start: 0.8776 (ttp) cc_final: 0.8548 (ttm) REVERT: B 251 ASP cc_start: 0.8096 (p0) cc_final: 0.7863 (p0) REVERT: A 433 HIS cc_start: 0.7357 (t-170) cc_final: 0.7154 (t-170) REVERT: A 893 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7168 (t0) REVERT: A 926 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 1197 ASP cc_start: 0.8203 (m-30) cc_final: 0.7896 (m-30) REVERT: A 1212 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8224 (tp) outliers start: 30 outliers final: 20 residues processed: 130 average time/residue: 0.2517 time to fit residues: 46.5252 Evaluate side-chains 128 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1027 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 0.0870 chunk 37 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.163654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.140227 restraints weight = 13740.374| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.20 r_work: 0.3163 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1767 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= 0.126 Angle : 0.516 9.795 15947 Z= 0.276 Chirality : 0.038 0.156 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.450 175.999 2002 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.10 % Allowed : 16.07 % 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: 0.91 (0.25), residues: 1247 helix: 1.70 (0.21), residues: 644 sheet: 0.50 (0.56), residues: 107 loop : -0.85 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 852 HIS 0.003 0.001 HIS B 265 PHE 0.014 0.001 PHE A 826 TYR 0.013 0.001 TYR B 161 ARG 0.001 0.000 ARG B 100 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 549) hydrogen bonds : angle 3.83069 ( 1513) covalent geometry : bond 0.00291 (11596) covalent geometry : angle 0.51601 (15947) *********************** 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 138 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7989 (mttt) cc_final: 0.7452 (ttpt) REVERT: B 60 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: B 100 ARG cc_start: 0.7732 (mtt90) cc_final: 0.7251 (mtp180) REVERT: B 114 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6852 (tt0) REVERT: B 168 MET cc_start: 0.8696 (ttp) cc_final: 0.8476 (ttm) REVERT: B 251 ASP cc_start: 0.8064 (p0) cc_final: 0.7810 (p0) REVERT: A 893 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6984 (t0) REVERT: A 926 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 1197 ASP cc_start: 0.8164 (m-30) cc_final: 0.7859 (m-30) REVERT: A 1212 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8174 (tp) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.2661 time to fit residues: 50.1900 Evaluate side-chains 128 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1027 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.160910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136507 restraints weight = 13780.628| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.23 r_work: 0.3115 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11596 Z= 0.180 Angle : 0.566 9.911 15947 Z= 0.302 Chirality : 0.040 0.170 1759 Planarity : 0.004 0.046 1835 Dihedral : 19.567 174.869 2002 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.56 % Allowed : 15.89 % 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: 0.71 (0.25), residues: 1247 helix: 1.49 (0.21), residues: 649 sheet: 0.39 (0.56), residues: 107 loop : -0.88 (0.28), residues: 491 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 0.002 PHE A 886 TYR 0.012 0.001 TYR A 805 ARG 0.003 0.000 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 549) hydrogen bonds : angle 4.00368 ( 1513) covalent geometry : bond 0.00430 (11596) covalent geometry : angle 0.56600 (15947) ********************** 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: 28 poor density : 106 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8051 (mttt) cc_final: 0.7444 (ttpt) REVERT: B 60 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: B 100 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7272 (mtp180) REVERT: B 114 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6914 (tt0) REVERT: B 168 MET cc_start: 0.8773 (ttp) cc_final: 0.8552 (ttm) REVERT: B 251 ASP cc_start: 0.8077 (p0) cc_final: 0.7829 (p0) REVERT: A 893 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7145 (t0) REVERT: A 926 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 1197 ASP cc_start: 0.8195 (m-30) cc_final: 0.7882 (m-30) REVERT: A 1212 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8253 (tp) outliers start: 28 outliers final: 22 residues processed: 129 average time/residue: 0.3520 time to fit residues: 67.2640 Evaluate side-chains 130 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 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 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 1027 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.161263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.137248 restraints weight = 13788.429| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.22 r_work: 0.3128 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1767 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= 0.141 Angle : 0.534 9.871 15947 Z= 0.285 Chirality : 0.039 0.155 1759 Planarity : 0.004 0.047 1835 Dihedral : 19.498 175.469 2002 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.37 % Allowed : 15.98 % 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: 0.81 (0.25), residues: 1247 helix: 1.56 (0.21), residues: 651 sheet: 0.43 (0.56), residues: 107 loop : -0.83 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 852 HIS 0.006 0.001 HIS A 433 PHE 0.014 0.001 PHE A 826 TYR 0.012 0.001 TYR B 161 ARG 0.001 0.000 ARG B 100 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 549) hydrogen bonds : angle 3.91163 ( 1513) covalent geometry : bond 0.00329 (11596) covalent geometry : angle 0.53361 (15947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5052.36 seconds wall clock time: 90 minutes 13.07 seconds (5413.07 seconds total)