Starting phenix.real_space_refine on Sat Oct 11 04:04:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6y_41084/10_2025/8t6y_41084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6y_41084/10_2025/8t6y_41084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6y_41084/10_2025/8t6y_41084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6y_41084/10_2025/8t6y_41084.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6y_41084/10_2025/8t6y_41084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6y_41084/10_2025/8t6y_41084.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 109 5.49 5 S 18 5.16 5 C 6916 2.51 5 N 1994 2.21 5 O 2445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11482 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1148, 9165 Classifications: {'peptide': 1148} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 32, 'TRANS': 1115} Chain breaks: 5 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 8, 'GLU:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1885 Classifications: {'RNA': 88} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 77} Chain: "C" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "D" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 3.18, per 1000 atoms: 0.28 Number of scatterers: 11482 At special positions: 0 Unit cell: (85.8196, 118.314, 122.48, 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 18 16.00 P 109 15.00 O 2445 8.00 N 1994 7.00 C 6916 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: 1.05 Conformation dependent library (CDL) restraints added in 449.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 7 sheets defined 55.4% alpha, 9.8% beta 34 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.742A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.860A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.600A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.715A pdb=" N ILE A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 271 through 283 Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 307 through 311 removed outlier: 4.229A pdb=" N THR A 310 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.643A pdb=" N LEU A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 removed outlier: 3.521A pdb=" N VAL A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.549A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.182A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.529A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.519A pdb=" N GLU A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 481 " --> pdb=" O PHE A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.618A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.786A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.708A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.390A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 removed outlier: 4.411A pdb=" N GLN A 650 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.595A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.611A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.879A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 940 removed outlier: 4.129A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.895A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.468A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.922A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.548A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1261 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 4.216A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.817A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.019A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.410A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA4, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.675A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.827A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.827A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3006 1.34 - 1.46: 3434 1.46 - 1.59: 5245 1.59 - 1.71: 211 1.71 - 1.83: 34 Bond restraints: 11930 Sorted by residual: bond pdb=" CB PRO A 503 " pdb=" CG PRO A 503 " ideal model delta sigma weight residual 1.492 1.637 -0.145 5.00e-02 4.00e+02 8.40e+00 bond pdb=" CB ASP A 284 " pdb=" CG ASP A 284 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.81e+00 bond pdb=" CB ASP A 298 " pdb=" CG ASP A 298 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.31e+00 bond pdb=" CG PRO A 503 " pdb=" CD PRO A 503 " ideal model delta sigma weight residual 1.503 1.442 0.061 3.40e-02 8.65e+02 3.26e+00 bond pdb=" CB LYS A 961 " pdb=" CG LYS A 961 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.65e+00 ... (remaining 11925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 16438 3.90 - 7.80: 157 7.80 - 11.70: 25 11.70 - 15.61: 6 15.61 - 19.51: 1 Bond angle restraints: 16627 Sorted by residual: angle pdb=" CA PRO A 503 " pdb=" N PRO A 503 " pdb=" CD PRO A 503 " ideal model delta sigma weight residual 112.00 98.96 13.04 1.40e+00 5.10e-01 8.67e+01 angle pdb=" CA LEU A1257 " pdb=" CB LEU A1257 " pdb=" CG LEU A1257 " ideal model delta sigma weight residual 116.30 135.81 -19.51 3.50e+00 8.16e-02 3.11e+01 angle pdb=" CA LYS A 599 " pdb=" CB LYS A 599 " pdb=" CG LYS A 599 " ideal model delta sigma weight residual 114.10 124.23 -10.13 2.00e+00 2.50e-01 2.56e+01 angle pdb=" CA MET A 694 " pdb=" CB MET A 694 " pdb=" CG MET A 694 " ideal model delta sigma weight residual 114.10 124.19 -10.09 2.00e+00 2.50e-01 2.55e+01 angle pdb=" CA LYS A 961 " pdb=" CB LYS A 961 " pdb=" CG LYS A 961 " ideal model delta sigma weight residual 114.10 123.97 -9.87 2.00e+00 2.50e-01 2.44e+01 ... (remaining 16622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 6642 29.78 - 59.56: 500 59.56 - 89.34: 85 89.34 - 119.12: 0 119.12 - 148.90: 1 Dihedral angle restraints: 7228 sinusoidal: 3853 harmonic: 3375 Sorted by residual: dihedral pdb=" CA PHE A 643 " pdb=" C PHE A 643 " pdb=" N ASP A 644 " pdb=" CA ASP A 644 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA MET A1089 " pdb=" C MET A1089 " pdb=" N PRO A1090 " pdb=" CA PRO A1090 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP A 603 " pdb=" C ASP A 603 " pdb=" N LYS A 604 " pdb=" CA LYS A 604 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 7225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1546 0.054 - 0.108: 307 0.108 - 0.162: 78 0.162 - 0.216: 10 0.216 - 0.270: 2 Chirality restraints: 1943 Sorted by residual: chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CG LEU A 623 " pdb=" CB LEU A 623 " pdb=" CD1 LEU A 623 " pdb=" CD2 LEU A 623 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA ASP A 304 " pdb=" N ASP A 304 " pdb=" C ASP A 304 " pdb=" CB ASP A 304 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 ... (remaining 1940 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 502 " 0.082 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 503 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 66 " -0.023 2.00e-02 2.50e+03 2.57e-02 1.48e+01 pdb=" N1 U B 66 " 0.061 2.00e-02 2.50e+03 pdb=" C2 U B 66 " -0.038 2.00e-02 2.50e+03 pdb=" O2 U B 66 " 0.009 2.00e-02 2.50e+03 pdb=" N3 U B 66 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 66 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B 66 " 0.000 2.00e-02 2.50e+03 pdb=" C5 U B 66 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U B 66 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 13 " 0.000 2.00e-02 2.50e+03 1.80e-02 8.88e+00 pdb=" N9 A B 13 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A B 13 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A B 13 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 13 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 13 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 13 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A B 13 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A B 13 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B 13 " 0.001 2.00e-02 2.50e+03 pdb=" C4 A B 13 " -0.044 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1139 2.75 - 3.29: 10855 3.29 - 3.82: 20288 3.82 - 4.36: 23742 4.36 - 4.90: 37900 Nonbonded interactions: 93924 Sorted by model distance: nonbonded pdb=" O VAL A 620 " pdb=" OG1 THR A 624 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR A1167 " pdb=" OE1 GLU A1170 " model vdw 2.255 3.040 nonbonded pdb=" OG SER A 541 " pdb=" OE1 GLN A 544 " model vdw 2.270 3.040 nonbonded pdb=" O SER A1088 " pdb=" OG SER A1088 " model vdw 2.311 3.040 nonbonded pdb=" NH2 ARG A1114 " pdb=" OP1 DG D 41 " model vdw 2.316 3.120 ... (remaining 93919 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=0.00 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.040 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 0.145 11930 Z= 0.207 Angle : 0.978 19.508 16627 Z= 0.491 Chirality : 0.048 0.270 1943 Planarity : 0.007 0.114 1722 Dihedral : 18.638 148.895 5040 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.13 % Allowed : 25.31 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.23), residues: 1136 helix: -0.82 (0.20), residues: 563 sheet: -0.38 (0.52), residues: 112 loop : -0.65 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 220 TYR 0.040 0.003 TYR A1001 PHE 0.034 0.002 PHE A 569 TRP 0.014 0.002 TRP A 464 HIS 0.008 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00480 (11930) covalent geometry : angle 0.97757 (16627) hydrogen bonds : bond 0.13253 ( 510) hydrogen bonds : angle 6.59914 ( 1446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8452 (tp30) cc_final: 0.7972 (tp30) REVERT: A 220 ARG cc_start: 0.8972 (ptm160) cc_final: 0.8627 (ttp80) REVERT: A 959 LYS cc_start: 0.6375 (pttt) cc_final: 0.5683 (ptpp) REVERT: A 970 PHE cc_start: 0.7237 (m-10) cc_final: 0.6934 (m-10) outliers start: 11 outliers final: 3 residues processed: 67 average time/residue: 0.5150 time to fit residues: 38.3092 Evaluate side-chains 56 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 670 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 544 GLN A 709 GLN A 971 GLN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.063213 restraints weight = 25697.478| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.04 r_work: 0.2748 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11930 Z= 0.223 Angle : 0.619 10.678 16627 Z= 0.321 Chirality : 0.041 0.187 1943 Planarity : 0.004 0.049 1722 Dihedral : 18.607 154.822 2803 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.71 % Allowed : 18.03 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.25), residues: 1136 helix: 0.41 (0.22), residues: 556 sheet: -0.18 (0.51), residues: 113 loop : -0.37 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1114 TYR 0.016 0.002 TYR A 521 PHE 0.021 0.002 PHE A1105 TRP 0.011 0.001 TRP A 476 HIS 0.007 0.002 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00501 (11930) covalent geometry : angle 0.61914 (16627) hydrogen bonds : bond 0.04227 ( 510) hydrogen bonds : angle 4.78599 ( 1446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8624 (tp30) cc_final: 0.8032 (tp30) REVERT: A 190 GLN cc_start: 0.9371 (mt0) cc_final: 0.9131 (mp10) REVERT: A 217 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8525 (t) REVERT: A 331 ASP cc_start: 0.8977 (m-30) cc_final: 0.8697 (m-30) REVERT: A 682 PHE cc_start: 0.9004 (m-80) cc_final: 0.8649 (m-10) REVERT: A 724 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6715 (pt) REVERT: A 1205 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: A 1325 LYS cc_start: 0.8593 (ptmm) cc_final: 0.7862 (tttp) REVERT: A 1343 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8705 (mm) outliers start: 46 outliers final: 15 residues processed: 108 average time/residue: 0.5392 time to fit residues: 63.8375 Evaluate side-chains 71 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1205 GLU Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.063670 restraints weight = 25760.361| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.03 r_work: 0.2773 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11930 Z= 0.151 Angle : 0.541 9.164 16627 Z= 0.283 Chirality : 0.038 0.179 1943 Planarity : 0.004 0.046 1722 Dihedral : 18.605 155.282 2801 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.28 % Allowed : 20.18 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1136 helix: 0.82 (0.23), residues: 562 sheet: 0.06 (0.52), residues: 111 loop : -0.29 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.021 0.001 TYR A1242 PHE 0.014 0.001 PHE A 432 TRP 0.009 0.001 TRP A 476 HIS 0.006 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00336 (11930) covalent geometry : angle 0.54087 (16627) hydrogen bonds : bond 0.03770 ( 510) hydrogen bonds : angle 4.52261 ( 1446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8562 (tp30) cc_final: 0.8022 (tp30) REVERT: A 331 ASP cc_start: 0.8981 (m-30) cc_final: 0.8681 (m-30) REVERT: A 724 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6693 (pt) REVERT: A 1047 LYS cc_start: 0.4143 (pptt) cc_final: 0.3850 (tmtt) REVERT: A 1118 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8839 (tppp) REVERT: A 1325 LYS cc_start: 0.8666 (ptmm) cc_final: 0.7997 (tttp) REVERT: A 1343 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8637 (mm) outliers start: 32 outliers final: 13 residues processed: 89 average time/residue: 0.5173 time to fit residues: 50.6638 Evaluate side-chains 64 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.099804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.064480 restraints weight = 25649.864| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.01 r_work: 0.2778 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11930 Z= 0.127 Angle : 0.519 9.560 16627 Z= 0.270 Chirality : 0.037 0.177 1943 Planarity : 0.003 0.046 1722 Dihedral : 18.533 154.914 2799 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.97 % Allowed : 20.59 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.25), residues: 1136 helix: 1.00 (0.22), residues: 568 sheet: 0.10 (0.52), residues: 111 loop : -0.17 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 220 TYR 0.016 0.001 TYR A1242 PHE 0.017 0.001 PHE A 682 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00280 (11930) covalent geometry : angle 0.51860 (16627) hydrogen bonds : bond 0.03480 ( 510) hydrogen bonds : angle 4.36428 ( 1446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8540 (tp30) cc_final: 0.7990 (tp30) REVERT: A 202 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8856 (t0) REVERT: A 220 ARG cc_start: 0.8987 (ptm160) cc_final: 0.8614 (ttp80) REVERT: A 331 ASP cc_start: 0.8996 (m-30) cc_final: 0.8700 (m-30) REVERT: A 723 HIS cc_start: 0.6800 (m-70) cc_final: 0.6589 (m90) REVERT: A 724 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6773 (pt) REVERT: A 926 GLN cc_start: 0.4418 (OUTLIER) cc_final: 0.3855 (tm130) REVERT: A 1047 LYS cc_start: 0.4267 (pptt) cc_final: 0.3944 (tmtt) REVERT: A 1325 LYS cc_start: 0.8704 (ptmm) cc_final: 0.7986 (tttp) REVERT: A 1343 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8651 (mm) outliers start: 29 outliers final: 15 residues processed: 84 average time/residue: 0.5290 time to fit residues: 48.8787 Evaluate side-chains 70 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 56 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 overall best weight: 2.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 GLN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.059501 restraints weight = 25814.120| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.01 r_work: 0.2682 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 11930 Z= 0.299 Angle : 0.638 12.605 16627 Z= 0.330 Chirality : 0.042 0.193 1943 Planarity : 0.004 0.045 1722 Dihedral : 18.776 154.746 2799 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.69 % Allowed : 19.88 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1136 helix: 0.91 (0.22), residues: 563 sheet: -0.07 (0.50), residues: 111 loop : -0.31 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 220 TYR 0.015 0.002 TYR A 155 PHE 0.023 0.002 PHE A1105 TRP 0.011 0.001 TRP A 476 HIS 0.009 0.002 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00673 (11930) covalent geometry : angle 0.63849 (16627) hydrogen bonds : bond 0.04565 ( 510) hydrogen bonds : angle 4.58666 ( 1446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8662 (tp30) cc_final: 0.8023 (tp30) REVERT: A 90 MET cc_start: 0.9146 (tpp) cc_final: 0.8750 (ttp) REVERT: A 202 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8859 (t0) REVERT: A 217 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8575 (t) REVERT: A 331 ASP cc_start: 0.9010 (m-30) cc_final: 0.8704 (m-30) REVERT: A 926 GLN cc_start: 0.4722 (OUTLIER) cc_final: 0.4124 (tm130) REVERT: A 1047 LYS cc_start: 0.4390 (pptt) cc_final: 0.4055 (tmtt) REVERT: A 1099 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8561 (mm-30) REVERT: A 1205 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: A 1325 LYS cc_start: 0.8803 (ptmm) cc_final: 0.8142 (tttp) REVERT: A 1343 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8806 (mm) outliers start: 36 outliers final: 12 residues processed: 93 average time/residue: 0.6082 time to fit residues: 61.3767 Evaluate side-chains 68 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1205 GLU Chi-restraints excluded: chain A residue 1269 ILE Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 556 ASN A 563 GLN A1066 ASN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.097796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062330 restraints weight = 25740.129| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.00 r_work: 0.2747 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11930 Z= 0.133 Angle : 0.535 12.379 16627 Z= 0.277 Chirality : 0.038 0.183 1943 Planarity : 0.003 0.051 1722 Dihedral : 18.614 156.267 2797 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.25 % Allowed : 21.62 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.25), residues: 1136 helix: 1.10 (0.23), residues: 567 sheet: 0.07 (0.52), residues: 109 loop : -0.15 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 220 TYR 0.013 0.001 TYR A1242 PHE 0.014 0.001 PHE A1105 TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00297 (11930) covalent geometry : angle 0.53526 (16627) hydrogen bonds : bond 0.03554 ( 510) hydrogen bonds : angle 4.34971 ( 1446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8548 (tp30) cc_final: 0.8093 (tp30) REVERT: A 190 GLN cc_start: 0.9339 (mt0) cc_final: 0.9088 (mp10) REVERT: A 202 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8898 (t0) REVERT: A 331 ASP cc_start: 0.9008 (m-30) cc_final: 0.8695 (m-30) REVERT: A 556 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.7913 (p0) REVERT: A 569 PHE cc_start: 0.9178 (m-80) cc_final: 0.8949 (m-80) REVERT: A 723 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6696 (m90) REVERT: A 1047 LYS cc_start: 0.4440 (pptt) cc_final: 0.4174 (tmtt) REVERT: A 1099 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8525 (mm-30) REVERT: A 1325 LYS cc_start: 0.8811 (ptmm) cc_final: 0.8164 (tttp) REVERT: A 1343 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8655 (mm) outliers start: 22 outliers final: 8 residues processed: 80 average time/residue: 0.5546 time to fit residues: 48.6605 Evaluate side-chains 64 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1269 ILE Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 0.0050 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 114 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 11 optimal weight: 0.0070 chunk 77 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 971 GLN A1066 ASN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.099585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.064539 restraints weight = 25579.156| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.02 r_work: 0.2798 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11930 Z= 0.104 Angle : 0.521 15.166 16627 Z= 0.267 Chirality : 0.037 0.195 1943 Planarity : 0.003 0.050 1722 Dihedral : 18.470 154.863 2797 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.36 % Allowed : 21.82 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.25), residues: 1136 helix: 1.30 (0.23), residues: 560 sheet: 0.05 (0.50), residues: 111 loop : -0.06 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 220 TYR 0.013 0.001 TYR A1242 PHE 0.010 0.001 PHE A 682 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00224 (11930) covalent geometry : angle 0.52132 (16627) hydrogen bonds : bond 0.03258 ( 510) hydrogen bonds : angle 4.19254 ( 1446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8450 (tp30) cc_final: 0.7899 (tp30) REVERT: A 190 GLN cc_start: 0.9315 (mt0) cc_final: 0.9062 (mp10) REVERT: A 331 ASP cc_start: 0.9001 (m-30) cc_final: 0.8705 (m-30) REVERT: A 1047 LYS cc_start: 0.4580 (pptt) cc_final: 0.4353 (tmtt) REVERT: A 1099 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8539 (mm-30) REVERT: A 1325 LYS cc_start: 0.8831 (ptmm) cc_final: 0.8230 (tttp) REVERT: A 1343 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8633 (mm) outliers start: 23 outliers final: 8 residues processed: 87 average time/residue: 0.4932 time to fit residues: 47.6368 Evaluate side-chains 64 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1269 ILE Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 563 GLN ** A1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.061205 restraints weight = 25693.019| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.00 r_work: 0.2726 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11930 Z= 0.189 Angle : 0.583 14.616 16627 Z= 0.294 Chirality : 0.039 0.213 1943 Planarity : 0.003 0.054 1722 Dihedral : 18.567 155.285 2797 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.84 % Allowed : 23.57 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1136 helix: 1.29 (0.23), residues: 560 sheet: 0.09 (0.50), residues: 111 loop : -0.14 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 220 TYR 0.014 0.001 TYR A 155 PHE 0.017 0.001 PHE A1105 TRP 0.007 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00426 (11930) covalent geometry : angle 0.58253 (16627) hydrogen bonds : bond 0.03858 ( 510) hydrogen bonds : angle 4.30027 ( 1446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8570 (tp30) cc_final: 0.8133 (tp30) REVERT: A 190 GLN cc_start: 0.9328 (mt0) cc_final: 0.9087 (mp10) REVERT: A 284 ASP cc_start: 0.9067 (p0) cc_final: 0.8547 (OUTLIER) REVERT: A 331 ASP cc_start: 0.9009 (m-30) cc_final: 0.8715 (m-30) REVERT: A 556 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8023 (p0) REVERT: A 1047 LYS cc_start: 0.4627 (pptt) cc_final: 0.4346 (tmtt) REVERT: A 1099 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8543 (mm-30) REVERT: A 1325 LYS cc_start: 0.8852 (ptmm) cc_final: 0.8254 (tttp) REVERT: A 1326 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6558 (t80) REVERT: A 1343 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8685 (mm) outliers start: 18 outliers final: 11 residues processed: 74 average time/residue: 0.5618 time to fit residues: 45.6248 Evaluate side-chains 68 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 35 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1066 ASN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.098477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.063430 restraints weight = 25461.789| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.00 r_work: 0.2776 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11930 Z= 0.118 Angle : 0.549 15.248 16627 Z= 0.275 Chirality : 0.037 0.202 1943 Planarity : 0.003 0.057 1722 Dihedral : 18.479 155.764 2797 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.84 % Allowed : 23.87 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.25), residues: 1136 helix: 1.36 (0.23), residues: 561 sheet: 0.10 (0.49), residues: 111 loop : -0.09 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 220 TYR 0.012 0.001 TYR A1242 PHE 0.012 0.001 PHE A 518 TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00262 (11930) covalent geometry : angle 0.54942 (16627) hydrogen bonds : bond 0.03417 ( 510) hydrogen bonds : angle 4.19339 ( 1446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8508 (tp30) cc_final: 0.7961 (tp30) REVERT: A 284 ASP cc_start: 0.9039 (p0) cc_final: 0.8566 (OUTLIER) REVERT: A 331 ASP cc_start: 0.9000 (m-30) cc_final: 0.8720 (m-30) REVERT: A 724 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6837 (pp) REVERT: A 1047 LYS cc_start: 0.4633 (pptt) cc_final: 0.4363 (tmtt) REVERT: A 1099 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8520 (mm-30) REVERT: A 1325 LYS cc_start: 0.8887 (ptmm) cc_final: 0.8278 (tttp) REVERT: A 1343 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8676 (mm) outliers start: 18 outliers final: 13 residues processed: 73 average time/residue: 0.5141 time to fit residues: 41.5670 Evaluate side-chains 69 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 251 ASN ** A1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.095398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.059883 restraints weight = 25649.473| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.99 r_work: 0.2684 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11930 Z= 0.245 Angle : 0.618 15.110 16627 Z= 0.313 Chirality : 0.041 0.217 1943 Planarity : 0.004 0.058 1722 Dihedral : 18.662 155.574 2797 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.64 % Allowed : 23.67 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.25), residues: 1136 helix: 1.22 (0.23), residues: 560 sheet: 0.09 (0.49), residues: 111 loop : -0.20 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 220 TYR 0.014 0.001 TYR A1242 PHE 0.020 0.002 PHE A1105 TRP 0.009 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00553 (11930) covalent geometry : angle 0.61772 (16627) hydrogen bonds : bond 0.04136 ( 510) hydrogen bonds : angle 4.37053 ( 1446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8602 (tp30) cc_final: 0.8161 (tp30) REVERT: A 90 MET cc_start: 0.9067 (tpp) cc_final: 0.8539 (ttp) REVERT: A 284 ASP cc_start: 0.9103 (p0) cc_final: 0.8717 (t0) REVERT: A 331 ASP cc_start: 0.9037 (m-30) cc_final: 0.8746 (m-30) REVERT: A 724 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.6918 (pp) REVERT: A 1047 LYS cc_start: 0.4719 (pptt) cc_final: 0.4517 (pptt) REVERT: A 1099 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8593 (mm-30) REVERT: A 1325 LYS cc_start: 0.8896 (ptmm) cc_final: 0.8325 (tttp) REVERT: A 1343 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8780 (mm) outliers start: 16 outliers final: 9 residues processed: 67 average time/residue: 0.5814 time to fit residues: 42.7391 Evaluate side-chains 63 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 58 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 612 ASN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.098336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.063417 restraints weight = 25485.376| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.97 r_work: 0.2765 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11930 Z= 0.114 Angle : 0.551 15.415 16627 Z= 0.277 Chirality : 0.037 0.205 1943 Planarity : 0.003 0.060 1722 Dihedral : 18.496 156.172 2797 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.13 % Allowed : 24.18 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.25), residues: 1136 helix: 1.36 (0.23), residues: 562 sheet: 0.12 (0.49), residues: 111 loop : -0.11 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 220 TYR 0.013 0.001 TYR A1242 PHE 0.013 0.001 PHE A 518 TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00251 (11930) covalent geometry : angle 0.55092 (16627) hydrogen bonds : bond 0.03403 ( 510) hydrogen bonds : angle 4.19387 ( 1446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3222.39 seconds wall clock time: 55 minutes 56.48 seconds (3356.48 seconds total)