Starting phenix.real_space_refine on Sat Jul 20 16:18:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5u_16443/07_2024/8c5u_16443.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5u_16443/07_2024/8c5u_16443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5u_16443/07_2024/8c5u_16443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5u_16443/07_2024/8c5u_16443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5u_16443/07_2024/8c5u_16443.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5u_16443/07_2024/8c5u_16443.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 35 5.16 5 C 7075 2.51 5 N 1984 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 115": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A TYR 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 934": "OE1" <-> "OE2" Residue "A ARG 1063": "NH1" <-> "NH2" Residue "A GLU 1224": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11419 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2698 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 7224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7224 Classifications: {'peptide': 919} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 44, 'TRANS': 874} Chain breaks: 3 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 663 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 152 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 6} Chain: "C" 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: 6.91, per 1000 atoms: 0.61 Number of scatterers: 11419 At special positions: 0 Unit cell: (105.73, 117.37, 118.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 74 15.00 O 2251 8.00 N 1984 7.00 C 7075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2362 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 60.3% alpha, 7.5% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.939A pdb=" N LEU B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.867A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.785A pdb=" N MET B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.623A pdb=" N GLU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.663A pdb=" N GLU B 233 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 234 " --> pdb=" O ALA B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 234' Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 273 through 278 removed outlier: 4.230A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.610A pdb=" N MET B 329 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 397 through 421 removed outlier: 4.500A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 449 through 478 Proline residue: A 463 - end of helix removed outlier: 3.831A pdb=" N GLU A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 497 removed outlier: 3.905A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.664A pdb=" N LYS A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 552 removed outlier: 3.831A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 removed outlier: 3.654A pdb=" N VAL A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 663 Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 737 through 751 removed outlier: 3.568A pdb=" N VAL A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 814 Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 857 through 873 removed outlier: 4.443A pdb=" N LEU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 4.928A 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 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 932 through 935 Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.615A pdb=" N GLN A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 997 Processing helix chain 'A' and resid 998 through 1005 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.055A pdb=" N VAL A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN A1015 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR A1016 " --> pdb=" O VAL A1012 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 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 1047 through 1066 Processing helix chain 'A' and resid 1067 through 1085 removed outlier: 3.539A pdb=" N ILE A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1094 Processing helix chain 'A' and resid 1149 through 1181 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1194 through 1196 No H-bonds generated for 'chain 'A' and resid 1194 through 1196' Processing helix chain 'A' and resid 1197 through 1214 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1260 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1293 removed outlier: 3.501A pdb=" N ARG A1287 " --> pdb=" O LEU A1283 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A1288 " --> pdb=" O ILE A1284 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A1289 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1300 removed outlier: 3.584A pdb=" N LEU A1299 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A1300 " --> pdb=" O THR A1296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1295 through 1300' Processing helix chain 'A' and resid 1305 through 1310 removed outlier: 3.558A pdb=" N LEU A1309 " --> pdb=" O ASP A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1346 Processing sheet with id=AA1, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.949A pdb=" N LEU B 98 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU B 75 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 50 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU B 76 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP B 52 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 206 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU B 246 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 204 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP B 248 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 202 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ILE B 227 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE B 205 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 619 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA6, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AA7, first strand: chain 'A' and resid 942 through 944 Processing sheet with id=AA8, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB1, first strand: chain 'A' and resid 1128 through 1131 removed outlier: 3.679A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 5.81 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: 2672 1.33 - 1.45: 2719 1.45 - 1.57: 6243 1.57 - 1.69: 141 1.69 - 1.81: 60 Bond restraints: 11835 Sorted by residual: bond pdb=" O3' DT T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 1.607 1.704 -0.097 1.50e-02 4.44e+03 4.21e+01 bond pdb=" C1' DA N 132 " pdb=" N9 DA N 132 " ideal model delta sigma weight residual 1.460 1.374 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" O3' DC T 11 " pdb=" P DA T 12 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.50e-02 4.44e+03 1.38e+01 bond pdb=" N VAL A 627 " pdb=" CA VAL A 627 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.18e-02 7.18e+03 9.42e+00 bond pdb=" N LYS A1007 " pdb=" CA LYS A1007 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.53e+00 ... (remaining 11830 not shown) Histogram of bond angle deviations from ideal: 98.88 - 106.21: 722 106.21 - 113.54: 6543 113.54 - 120.87: 5603 120.87 - 128.20: 3281 128.20 - 135.53: 199 Bond angle restraints: 16348 Sorted by residual: angle pdb=" C5' DC T 25 " pdb=" C4' DC T 25 " pdb=" O4' DC T 25 " ideal model delta sigma weight residual 109.40 118.99 -9.59 1.50e+00 4.44e-01 4.09e+01 angle pdb=" C TYR A 499 " pdb=" CA TYR A 499 " pdb=" CB TYR A 499 " ideal model delta sigma weight residual 110.44 101.95 8.49 1.68e+00 3.54e-01 2.55e+01 angle pdb=" PA GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PB GTP C 201 " ideal model delta sigma weight residual 120.50 135.53 -15.03 3.00e+00 1.11e-01 2.51e+01 angle pdb=" C3' DT T 20 " pdb=" O3' DT T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 120.20 112.88 7.32 1.50e+00 4.44e-01 2.38e+01 angle pdb=" O3' DA N 131 " pdb=" C3' DA N 131 " pdb=" C2' DA N 131 " ideal model delta sigma weight residual 111.50 104.99 6.51 1.50e+00 4.44e-01 1.89e+01 ... (remaining 16343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.60: 6485 29.60 - 59.19: 447 59.19 - 88.78: 37 88.78 - 118.38: 3 118.38 - 147.97: 4 Dihedral angle restraints: 6976 sinusoidal: 3332 harmonic: 3644 Sorted by residual: dihedral pdb=" O4' G C 108 " pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" C2' G C 108 " ideal model delta sinusoidal sigma weight residual 24.00 -30.76 54.76 1 8.00e+00 1.56e-02 6.35e+01 dihedral pdb=" C5' G C 108 " pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" O3' G C 108 " ideal model delta sinusoidal sigma weight residual 147.00 93.88 53.12 1 8.00e+00 1.56e-02 6.00e+01 dihedral pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" C2' G C 108 " pdb=" C1' G C 108 " ideal model delta sinusoidal sigma weight residual -35.00 13.18 -48.18 1 8.00e+00 1.56e-02 5.00e+01 ... (remaining 6973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1731 0.105 - 0.209: 70 0.209 - 0.314: 8 0.314 - 0.418: 1 0.418 - 0.523: 2 Chirality restraints: 1812 Sorted by residual: chirality pdb=" P DT T 41 " pdb=" OP1 DT T 41 " pdb=" OP2 DT T 41 " pdb=" O5' DT T 41 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" P DT N 111 " pdb=" OP1 DT N 111 " pdb=" OP2 DT N 111 " pdb=" O5' DT N 111 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" P G C 102 " pdb=" OP1 G C 102 " pdb=" OP2 G C 102 " pdb=" O5' G C 102 " both_signs ideal model delta sigma weight residual True 2.41 2.81 -0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 1809 not shown) Planarity restraints: 1833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1350 " -0.008 2.00e-02 2.50e+03 1.31e-02 3.02e+00 pdb=" CG PHE A1350 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A1350 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A1350 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A1350 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A1350 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A1350 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1337 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C ASP A1337 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP A1337 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A1338 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 15 " 0.016 2.00e-02 2.50e+03 8.85e-03 1.96e+00 pdb=" N1 DT T 15 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DT T 15 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT T 15 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT T 15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT T 15 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT T 15 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT T 15 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT T 15 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT T 15 " -0.010 2.00e-02 2.50e+03 ... (remaining 1830 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 751 2.73 - 3.27: 11289 3.27 - 3.82: 19694 3.82 - 4.36: 22850 4.36 - 4.90: 37585 Nonbonded interactions: 92169 Sorted by model distance: nonbonded pdb=" OD1 ASN A 842 " pdb=" OG SER A 845 " model vdw 2.189 2.440 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.206 2.440 nonbonded pdb=" O PRO B 102 " pdb=" OH TYR B 108 " model vdw 2.224 2.440 nonbonded pdb=" OE2 GLU A1125 " pdb=" OG SER A1140 " model vdw 2.281 2.440 nonbonded pdb=" OG SER B 124 " pdb=" OD1 ASP B 126 " model vdw 2.307 2.440 ... (remaining 92164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 39.400 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 0.097 11835 Z= 0.286 Angle : 0.774 15.031 16348 Z= 0.437 Chirality : 0.053 0.523 1812 Planarity : 0.004 0.034 1833 Dihedral : 18.428 147.972 4614 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 1.11 (0.24), residues: 1238 helix: 1.75 (0.20), residues: 677 sheet: -0.61 (0.49), residues: 110 loop : -0.42 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 159 HIS 0.007 0.001 HIS A 943 PHE 0.028 0.001 PHE A1350 TYR 0.016 0.001 TYR A 496 ARG 0.004 0.000 ARG A1151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: B 39 THR cc_start: 0.8684 (p) cc_final: 0.8133 (t) REVERT: B 209 ASP cc_start: 0.8343 (t0) cc_final: 0.8111 (t0) REVERT: B 329 MET cc_start: 0.7504 (tpp) cc_final: 0.7055 (tpp) REVERT: A 796 ASP cc_start: 0.8136 (m-30) cc_final: 0.7778 (m-30) REVERT: A 926 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 962 GLU cc_start: 0.8024 (tp30) cc_final: 0.7771 (tp30) REVERT: A 1007 LYS cc_start: 0.7761 (pttt) cc_final: 0.7502 (pttt) REVERT: A 1197 ASP cc_start: 0.8267 (m-30) cc_final: 0.8063 (m-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2387 time to fit residues: 60.0286 Evaluate side-chains 137 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 117 optimal weight: 50.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 308 ASN A 520 ASN A 791 ASN A 925 ASN A1070 HIS A1129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11835 Z= 0.209 Angle : 0.569 9.107 16348 Z= 0.302 Chirality : 0.040 0.158 1812 Planarity : 0.004 0.035 1833 Dihedral : 20.395 152.602 2195 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.41 % Allowed : 8.34 % Favored : 90.25 % 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: 1.30 (0.24), residues: 1238 helix: 1.96 (0.20), residues: 674 sheet: -0.52 (0.45), residues: 124 loop : -0.39 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 908 HIS 0.003 0.001 HIS A 953 PHE 0.017 0.001 PHE A1350 TYR 0.025 0.001 TYR A 496 ARG 0.002 0.000 ARG A1151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: B 209 ASP cc_start: 0.8266 (t0) cc_final: 0.7989 (t0) REVERT: B 329 MET cc_start: 0.7603 (tpp) cc_final: 0.7094 (tpp) REVERT: A 533 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8240 (ttp-170) REVERT: A 796 ASP cc_start: 0.8100 (m-30) cc_final: 0.7789 (m-30) REVERT: A 962 GLU cc_start: 0.8050 (tp30) cc_final: 0.7699 (tp30) REVERT: A 1078 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7073 (tm-30) REVERT: A 1197 ASP cc_start: 0.8293 (m-30) cc_final: 0.8091 (m-30) REVERT: A 1259 LEU cc_start: 0.8122 (tt) cc_final: 0.7603 (mt) outliers start: 15 outliers final: 11 residues processed: 157 average time/residue: 0.2305 time to fit residues: 52.4211 Evaluate side-chains 138 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 117 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 overall best weight: 6.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 308 ASN A 791 ASN A 925 ASN A1036 GLN A1070 HIS A1129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11835 Z= 0.343 Angle : 0.609 8.405 16348 Z= 0.323 Chirality : 0.041 0.150 1812 Planarity : 0.004 0.034 1833 Dihedral : 20.483 162.820 2195 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.72 % Allowed : 9.65 % Favored : 87.63 % 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: 1.05 (0.24), residues: 1238 helix: 1.74 (0.20), residues: 679 sheet: -0.57 (0.49), residues: 112 loop : -0.54 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 908 HIS 0.005 0.001 HIS A1188 PHE 0.019 0.001 PHE A1350 TYR 0.024 0.002 TYR A 496 ARG 0.006 0.001 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 209 ASP cc_start: 0.8285 (t0) cc_final: 0.8004 (t0) REVERT: B 329 MET cc_start: 0.7681 (tpp) cc_final: 0.7307 (tpp) REVERT: A 533 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8433 (ttp-170) REVERT: A 796 ASP cc_start: 0.8105 (m-30) cc_final: 0.7884 (m-30) REVERT: A 962 GLU cc_start: 0.8128 (tp30) cc_final: 0.7804 (tp30) REVERT: A 1015 GLN cc_start: 0.8037 (mm110) cc_final: 0.7787 (mm-40) REVERT: A 1197 ASP cc_start: 0.8446 (m-30) cc_final: 0.8234 (m-30) REVERT: A 1259 LEU cc_start: 0.8097 (tt) cc_final: 0.7579 (mp) outliers start: 29 outliers final: 21 residues processed: 148 average time/residue: 0.2262 time to fit residues: 49.0199 Evaluate side-chains 143 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 0.0470 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN A1070 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11835 Z= 0.200 Angle : 0.547 8.071 16348 Z= 0.291 Chirality : 0.039 0.158 1812 Planarity : 0.003 0.034 1833 Dihedral : 20.303 170.783 2195 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.34 % Allowed : 12.00 % Favored : 85.66 % 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: 1.20 (0.24), residues: 1238 helix: 1.88 (0.20), residues: 683 sheet: -0.14 (0.54), residues: 98 loop : -0.62 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 908 HIS 0.005 0.001 HIS A 953 PHE 0.020 0.001 PHE A1350 TYR 0.027 0.001 TYR B 161 ARG 0.007 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 209 ASP cc_start: 0.8208 (t0) cc_final: 0.7909 (t0) REVERT: B 329 MET cc_start: 0.7677 (tpp) cc_final: 0.7297 (tpp) REVERT: A 533 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8355 (ttp-170) REVERT: A 796 ASP cc_start: 0.8094 (m-30) cc_final: 0.7800 (m-30) REVERT: A 962 GLU cc_start: 0.8038 (tp30) cc_final: 0.7711 (tp30) REVERT: A 1259 LEU cc_start: 0.8095 (tt) cc_final: 0.7532 (mp) outliers start: 25 outliers final: 16 residues processed: 148 average time/residue: 0.2579 time to fit residues: 55.3104 Evaluate side-chains 145 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A1070 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11835 Z= 0.327 Angle : 0.602 8.100 16348 Z= 0.317 Chirality : 0.041 0.158 1812 Planarity : 0.004 0.033 1833 Dihedral : 20.263 172.057 2195 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 2.72 % Allowed : 12.46 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1238 helix: 1.73 (0.19), residues: 683 sheet: -0.26 (0.54), residues: 98 loop : -0.69 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 908 HIS 0.004 0.001 HIS A1188 PHE 0.014 0.001 PHE A1349 TYR 0.016 0.001 TYR A 496 ARG 0.007 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 329 MET cc_start: 0.7700 (tpp) cc_final: 0.7324 (tpp) REVERT: A 796 ASP cc_start: 0.8115 (m-30) cc_final: 0.7855 (m-30) REVERT: A 962 GLU cc_start: 0.8113 (tp30) cc_final: 0.7823 (tp30) REVERT: A 1176 GLU cc_start: 0.8582 (tp30) cc_final: 0.8358 (tp30) REVERT: A 1259 LEU cc_start: 0.8045 (tt) cc_final: 0.7521 (mp) outliers start: 29 outliers final: 21 residues processed: 152 average time/residue: 0.2362 time to fit residues: 51.8118 Evaluate side-chains 147 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 120 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN A 804 ASN A 925 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11835 Z= 0.392 Angle : 0.635 8.991 16348 Z= 0.335 Chirality : 0.042 0.191 1812 Planarity : 0.004 0.034 1833 Dihedral : 20.115 145.897 2195 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 3.47 % Allowed : 13.31 % Favored : 83.22 % 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 (0.24), residues: 1238 helix: 1.51 (0.19), residues: 683 sheet: -0.38 (0.53), residues: 98 loop : -0.79 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 908 HIS 0.005 0.001 HIS A1188 PHE 0.016 0.002 PHE A1349 TYR 0.016 0.002 TYR A 496 ARG 0.008 0.001 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: B 111 LEU cc_start: 0.7726 (tp) cc_final: 0.7479 (tp) REVERT: B 141 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7827 (tm-30) REVERT: B 329 MET cc_start: 0.7672 (tpp) cc_final: 0.7320 (tpp) REVERT: A 533 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8510 (ttp-170) REVERT: A 796 ASP cc_start: 0.8093 (m-30) cc_final: 0.7831 (m-30) REVERT: A 962 GLU cc_start: 0.8164 (tp30) cc_final: 0.7890 (tp30) REVERT: A 1176 GLU cc_start: 0.8595 (tp30) cc_final: 0.8362 (tp30) REVERT: A 1259 LEU cc_start: 0.8058 (tt) cc_final: 0.7495 (mp) outliers start: 37 outliers final: 28 residues processed: 150 average time/residue: 0.2366 time to fit residues: 51.3195 Evaluate side-chains 154 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1288 ASN Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A1070 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11835 Z= 0.173 Angle : 0.564 9.572 16348 Z= 0.295 Chirality : 0.038 0.175 1812 Planarity : 0.003 0.034 1833 Dihedral : 19.507 144.114 2195 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 2.34 % Allowed : 14.15 % Favored : 83.51 % 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: 1.13 (0.24), residues: 1238 helix: 1.83 (0.20), residues: 684 sheet: -0.60 (0.49), residues: 108 loop : -0.57 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 908 HIS 0.004 0.001 HIS A 953 PHE 0.014 0.001 PHE A 826 TYR 0.016 0.001 TYR A 496 ARG 0.008 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 329 MET cc_start: 0.7629 (tpp) cc_final: 0.7261 (tpp) REVERT: A 533 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8383 (ttp-170) REVERT: A 592 TRP cc_start: 0.8478 (m-10) cc_final: 0.7502 (m100) REVERT: A 796 ASP cc_start: 0.8032 (m-30) cc_final: 0.7821 (m-30) REVERT: A 856 LYS cc_start: 0.8269 (mmtp) cc_final: 0.8050 (mmmm) REVERT: A 962 GLU cc_start: 0.8081 (tp30) cc_final: 0.7787 (tp30) REVERT: A 1176 GLU cc_start: 0.8522 (tp30) cc_final: 0.8306 (tp30) REVERT: A 1259 LEU cc_start: 0.8088 (tt) cc_final: 0.7526 (mp) outliers start: 25 outliers final: 18 residues processed: 157 average time/residue: 0.2513 time to fit residues: 56.7478 Evaluate side-chains 149 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1271 PHE Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11835 Z= 0.294 Angle : 0.597 9.661 16348 Z= 0.313 Chirality : 0.040 0.219 1812 Planarity : 0.004 0.033 1833 Dihedral : 19.530 145.953 2195 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 2.16 % Allowed : 15.28 % Favored : 82.57 % 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: 1.02 (0.24), residues: 1238 helix: 1.74 (0.20), residues: 684 sheet: -0.62 (0.49), residues: 110 loop : -0.63 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 908 HIS 0.003 0.001 HIS A1188 PHE 0.012 0.001 PHE A 826 TYR 0.029 0.001 TYR B 161 ARG 0.008 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 329 MET cc_start: 0.7651 (tpp) cc_final: 0.7283 (tpp) REVERT: A 533 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8353 (ttp-170) REVERT: A 796 ASP cc_start: 0.8155 (m-30) cc_final: 0.7905 (m-30) REVERT: A 962 GLU cc_start: 0.8137 (tp30) cc_final: 0.7856 (tp30) REVERT: A 1176 GLU cc_start: 0.8576 (tp30) cc_final: 0.8362 (tp30) REVERT: A 1259 LEU cc_start: 0.8064 (tt) cc_final: 0.7487 (mp) outliers start: 23 outliers final: 17 residues processed: 143 average time/residue: 0.2335 time to fit residues: 48.2312 Evaluate side-chains 144 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1271 PHE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN A 925 ASN A1070 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11835 Z= 0.273 Angle : 0.591 9.044 16348 Z= 0.310 Chirality : 0.040 0.210 1812 Planarity : 0.004 0.034 1833 Dihedral : 19.520 148.072 2195 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.07 % Favored : 96.85 % Rotamer: Outliers : 2.25 % Allowed : 15.18 % Favored : 82.57 % 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: 0.97 (0.24), residues: 1238 helix: 1.70 (0.20), residues: 684 sheet: -0.66 (0.48), residues: 110 loop : -0.63 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 908 HIS 0.004 0.001 HIS A 953 PHE 0.017 0.001 PHE A1350 TYR 0.016 0.001 TYR A 496 ARG 0.008 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 329 MET cc_start: 0.7638 (tpp) cc_final: 0.7273 (tpp) REVERT: A 533 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8352 (ttp-170) REVERT: A 796 ASP cc_start: 0.8165 (m-30) cc_final: 0.7888 (m-30) REVERT: A 962 GLU cc_start: 0.8130 (tp30) cc_final: 0.7852 (tp30) REVERT: A 1176 GLU cc_start: 0.8538 (tp30) cc_final: 0.8321 (tp30) REVERT: A 1259 LEU cc_start: 0.8072 (tt) cc_final: 0.7486 (mp) outliers start: 24 outliers final: 21 residues processed: 144 average time/residue: 0.2429 time to fit residues: 50.6096 Evaluate side-chains 151 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1271 PHE Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 0.0030 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN A 925 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11835 Z= 0.199 Angle : 0.574 8.781 16348 Z= 0.300 Chirality : 0.039 0.203 1812 Planarity : 0.004 0.034 1833 Dihedral : 19.441 150.159 2195 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 2.06 % Allowed : 15.46 % Favored : 82.47 % 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: 1.06 (0.24), residues: 1238 helix: 1.78 (0.20), residues: 684 sheet: -0.61 (0.49), residues: 110 loop : -0.61 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 908 HIS 0.003 0.001 HIS A 953 PHE 0.025 0.001 PHE A1350 TYR 0.015 0.001 TYR A 496 ARG 0.008 0.000 ARG A 533 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: B 141 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7797 (tm-30) REVERT: B 329 MET cc_start: 0.7605 (tpp) cc_final: 0.7245 (tpp) REVERT: A 533 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8327 (ttp-170) REVERT: A 592 TRP cc_start: 0.8492 (m-10) cc_final: 0.7507 (m100) REVERT: A 796 ASP cc_start: 0.8144 (m-30) cc_final: 0.7865 (m-30) REVERT: A 962 GLU cc_start: 0.8116 (tp30) cc_final: 0.7818 (tp30) REVERT: A 1259 LEU cc_start: 0.8073 (tt) cc_final: 0.7480 (mp) outliers start: 22 outliers final: 19 residues processed: 148 average time/residue: 0.2409 time to fit residues: 51.9338 Evaluate side-chains 147 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 40.0000 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095438 restraints weight = 20737.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098552 restraints weight = 11201.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100541 restraints weight = 7875.365| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11835 Z= 0.190 Angle : 0.576 8.518 16348 Z= 0.301 Chirality : 0.039 0.233 1812 Planarity : 0.004 0.034 1833 Dihedral : 19.368 151.621 2195 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.06 % Allowed : 15.46 % Favored : 82.47 % 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: 1.08 (0.24), residues: 1238 helix: 1.80 (0.20), residues: 684 sheet: -0.56 (0.49), residues: 110 loop : -0.62 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 908 HIS 0.003 0.001 HIS A 953 PHE 0.026 0.001 PHE A1350 TYR 0.030 0.001 TYR B 161 ARG 0.008 0.000 ARG A 533 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2077.97 seconds wall clock time: 38 minutes 13.00 seconds (2293.00 seconds total)