Starting phenix.real_space_refine on Tue Jul 29 16:33:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6y_41084/07_2025/8t6y_41084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6y_41084/07_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_41084/07_2025/8t6y_41084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6y_41084/07_2025/8t6y_41084.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6y_41084/07_2025/8t6y_41084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6y_41084/07_2025/8t6y_41084.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 8} 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: 8.29, per 1000 atoms: 0.72 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: 2.98 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.35 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: 5.61 Time building geometry restraints manager: 3.46 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: 20.550 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.640 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.970 ------------------------------------------------------------------------------- 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 (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: -1.21 (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 TRP 0.014 0.002 TRP A 464 HIS 0.008 0.001 HIS A 129 PHE 0.034 0.002 PHE A 569 TYR 0.040 0.003 TYR A1001 ARG 0.019 0.002 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.13253 ( 510) hydrogen bonds : angle 6.59914 ( 1446) covalent geometry : bond 0.00480 (11930) covalent geometry : angle 0.97757 (16627) *********************** 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 : 1.069 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: 1.0401 time to fit residues: 77.7824 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 : 1.109 ------------------------------------------------------------------------------- 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 104 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 497 ASN A 544 GLN A 971 GLN A 980 ASN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.064122 restraints weight = 25412.829| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.01 r_work: 0.2761 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11930 Z= 0.218 Angle : 0.623 10.872 16627 Z= 0.322 Chirality : 0.041 0.189 1943 Planarity : 0.005 0.048 1722 Dihedral : 18.607 154.770 2803 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.61 % Allowed : 18.44 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1136 helix: 0.40 (0.22), residues: 556 sheet: -0.19 (0.51), residues: 113 loop : -0.38 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.007 0.002 HIS A 129 PHE 0.021 0.002 PHE A1105 TYR 0.016 0.002 TYR A 521 ARG 0.006 0.001 ARG A1114 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 510) hydrogen bonds : angle 4.80216 ( 1446) covalent geometry : bond 0.00492 (11930) covalent geometry : angle 0.62334 (16627) *********************** 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 110 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8612 (tp30) cc_final: 0.8021 (tp30) REVERT: A 217 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8531 (t) REVERT: A 331 ASP cc_start: 0.8945 (m-30) cc_final: 0.8669 (m-30) REVERT: A 682 PHE cc_start: 0.9007 (m-80) cc_final: 0.8642 (m-10) REVERT: A 724 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6727 (pt) REVERT: A 1205 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: A 1325 LYS cc_start: 0.8595 (ptmm) cc_final: 0.7867 (tttp) REVERT: A 1343 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8696 (mm) outliers start: 45 outliers final: 15 residues processed: 107 average time/residue: 1.4915 time to fit residues: 178.9398 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 : 1.459 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.4980 chunk 67 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 497 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 = 0.3643 r_free = 0.3643 target = 0.099917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.064162 restraints weight = 25636.082| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.03 r_work: 0.2786 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1894 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= 0.139 Angle : 0.533 9.195 16627 Z= 0.278 Chirality : 0.038 0.178 1943 Planarity : 0.004 0.046 1722 Dihedral : 18.586 155.228 2801 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.18 % Allowed : 20.18 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1136 helix: 0.79 (0.22), residues: 567 sheet: 0.09 (0.52), residues: 111 loop : -0.25 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.014 0.001 PHE A 432 TYR 0.013 0.001 TYR A 521 ARG 0.007 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 510) hydrogen bonds : angle 4.50576 ( 1446) covalent geometry : bond 0.00309 (11930) covalent geometry : angle 0.53303 (16627) *********************** 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 92 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8554 (tp30) cc_final: 0.8019 (tp30) REVERT: A 220 ARG cc_start: 0.9001 (ptm160) cc_final: 0.8662 (ttp80) REVERT: A 331 ASP cc_start: 0.8977 (m-30) cc_final: 0.8675 (m-30) REVERT: A 682 PHE cc_start: 0.9042 (m-80) cc_final: 0.8828 (m-10) REVERT: A 724 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6678 (pt) REVERT: A 1047 LYS cc_start: 0.4162 (pptt) cc_final: 0.3864 (tmtt) REVERT: A 1325 LYS cc_start: 0.8685 (ptmm) cc_final: 0.8009 (tttp) REVERT: A 1343 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8645 (mm) outliers start: 31 outliers final: 12 residues processed: 90 average time/residue: 1.0082 time to fit residues: 100.7116 Evaluate side-chains 64 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 1007 GLU 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 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.0010 chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1261 GLN ** 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 = 0.3619 r_free = 0.3619 target = 0.098327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.063150 restraints weight = 25502.085| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.00 r_work: 0.2746 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11930 Z= 0.169 Angle : 0.551 12.337 16627 Z= 0.285 Chirality : 0.038 0.181 1943 Planarity : 0.003 0.046 1722 Dihedral : 18.591 154.718 2799 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.97 % Allowed : 20.49 % 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 (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: 0.54 (0.25), residues: 1136 helix: 0.96 (0.22), residues: 568 sheet: 0.09 (0.51), residues: 111 loop : -0.19 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 PHE 0.016 0.001 PHE A1105 TYR 0.017 0.001 TYR A1242 ARG 0.007 0.000 ARG A1303 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 510) hydrogen bonds : angle 4.40907 ( 1446) covalent geometry : bond 0.00378 (11930) covalent geometry : angle 0.55062 (16627) *********************** 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 87 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8571 (tp30) cc_final: 0.8025 (tp30) REVERT: A 190 GLN cc_start: 0.9353 (mt0) cc_final: 0.9112 (mp10) REVERT: A 202 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8856 (t0) REVERT: A 331 ASP cc_start: 0.8999 (m-30) cc_final: 0.8699 (m-30) REVERT: A 1047 LYS cc_start: 0.4373 (pptt) cc_final: 0.4066 (tmtt) REVERT: A 1325 LYS cc_start: 0.8729 (ptmm) cc_final: 0.8046 (tttp) REVERT: A 1343 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8673 (mm) outliers start: 29 outliers final: 13 residues processed: 84 average time/residue: 1.0866 time to fit residues: 100.8559 Evaluate side-chains 65 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 733 ILE 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 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 108 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 0.0670 chunk 105 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3631 r_free = 0.3631 target = 0.099065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.063843 restraints weight = 25579.942| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.00 r_work: 0.2770 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11930 Z= 0.129 Angle : 0.521 11.214 16627 Z= 0.269 Chirality : 0.037 0.182 1943 Planarity : 0.003 0.046 1722 Dihedral : 18.540 155.479 2799 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.56 % Allowed : 21.00 % 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 (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: 0.75 (0.25), residues: 1136 helix: 1.14 (0.23), residues: 566 sheet: 0.10 (0.51), residues: 111 loop : -0.09 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.018 0.001 PHE A 682 TYR 0.014 0.001 TYR A1242 ARG 0.009 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 510) hydrogen bonds : angle 4.29767 ( 1446) covalent geometry : bond 0.00286 (11930) covalent geometry : angle 0.52050 (16627) *********************** 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 81 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8545 (tp30) cc_final: 0.7989 (tp30) REVERT: A 220 ARG cc_start: 0.8956 (ptm160) cc_final: 0.8680 (ttp80) REVERT: A 331 ASP cc_start: 0.9012 (m-30) cc_final: 0.8716 (m-30) REVERT: A 1047 LYS cc_start: 0.4556 (pptt) cc_final: 0.4200 (tmtt) REVERT: A 1205 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: A 1325 LYS cc_start: 0.8799 (ptmm) cc_final: 0.8138 (tttp) REVERT: A 1343 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8679 (mm) outliers start: 25 outliers final: 10 residues processed: 78 average time/residue: 1.1523 time to fit residues: 99.0581 Evaluate side-chains 63 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET 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 583 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR 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 1205 GLU 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 47 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 112 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 0.0020 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.099788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.065281 restraints weight = 25837.292| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.01 r_work: 0.2793 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11930 Z= 0.112 Angle : 0.499 10.031 16627 Z= 0.258 Chirality : 0.037 0.189 1943 Planarity : 0.003 0.043 1722 Dihedral : 18.452 154.877 2799 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.56 % Allowed : 20.70 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.90 (0.25), residues: 1136 helix: 1.29 (0.23), residues: 565 sheet: 0.12 (0.50), residues: 111 loop : -0.02 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.009 0.001 PHE A1105 TYR 0.013 0.001 TYR A1242 ARG 0.006 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 510) hydrogen bonds : angle 4.18871 ( 1446) covalent geometry : bond 0.00244 (11930) covalent geometry : angle 0.49944 (16627) *********************** 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 85 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8524 (tp30) cc_final: 0.7977 (tp30) REVERT: A 331 ASP cc_start: 0.9015 (m-30) cc_final: 0.8720 (m-30) REVERT: A 569 PHE cc_start: 0.9121 (m-80) cc_final: 0.8913 (m-80) REVERT: A 724 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6746 (pp) REVERT: A 1047 LYS cc_start: 0.4430 (pptt) cc_final: 0.4164 (tmtt) REVERT: A 1099 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8539 (mm-30) REVERT: A 1325 LYS cc_start: 0.8816 (ptmm) cc_final: 0.8195 (tttp) outliers start: 25 outliers final: 12 residues processed: 84 average time/residue: 0.9998 time to fit residues: 94.1411 Evaluate side-chains 65 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 524 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 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 1269 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 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 = 0.3628 r_free = 0.3628 target = 0.098752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.063716 restraints weight = 25936.043| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.00 r_work: 0.2769 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11930 Z= 0.133 Angle : 0.518 9.958 16627 Z= 0.266 Chirality : 0.037 0.197 1943 Planarity : 0.003 0.043 1722 Dihedral : 18.464 155.203 2799 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.74 % Allowed : 22.23 % Favored : 76.02 % 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: 0.92 (0.25), residues: 1136 helix: 1.33 (0.23), residues: 560 sheet: 0.14 (0.50), residues: 111 loop : -0.04 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 PHE 0.015 0.001 PHE A 518 TYR 0.013 0.001 TYR A1242 ARG 0.010 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 510) hydrogen bonds : angle 4.18457 ( 1446) covalent geometry : bond 0.00293 (11930) covalent geometry : angle 0.51835 (16627) *********************** 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 73 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8542 (tp30) cc_final: 0.7963 (tp30) REVERT: A 202 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8865 (t0) REVERT: A 331 ASP cc_start: 0.9023 (m-30) cc_final: 0.8743 (m-30) REVERT: A 724 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6773 (pp) REVERT: A 926 GLN cc_start: 0.4540 (OUTLIER) cc_final: 0.3936 (tm130) REVERT: A 1047 LYS cc_start: 0.4446 (pptt) cc_final: 0.4222 (tmtt) REVERT: A 1099 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8545 (mm-30) REVERT: A 1325 LYS cc_start: 0.8843 (ptmm) cc_final: 0.8238 (tttp) REVERT: A 1326 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.6516 (t80) outliers start: 17 outliers final: 11 residues processed: 70 average time/residue: 1.1343 time to fit residues: 87.8192 Evaluate side-chains 69 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 244 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 926 GLN 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 1269 ILE Chi-restraints excluded: chain A residue 1326 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 113 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3604 r_free = 0.3604 target = 0.097264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061998 restraints weight = 25848.136| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.98 r_work: 0.2737 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11930 Z= 0.167 Angle : 0.552 9.711 16627 Z= 0.283 Chirality : 0.038 0.203 1943 Planarity : 0.003 0.045 1722 Dihedral : 18.537 155.625 2799 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.56 % Allowed : 22.03 % Favored : 75.41 % 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: 0.86 (0.25), residues: 1136 helix: 1.26 (0.23), residues: 561 sheet: 0.17 (0.50), residues: 111 loop : -0.05 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 PHE 0.016 0.001 PHE A 518 TYR 0.014 0.001 TYR A1242 ARG 0.011 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 510) hydrogen bonds : angle 4.24768 ( 1446) covalent geometry : bond 0.00378 (11930) covalent geometry : angle 0.55185 (16627) *********************** 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 85 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8559 (tp30) cc_final: 0.8117 (tp30) REVERT: A 202 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8830 (t0) REVERT: A 284 ASP cc_start: 0.9068 (p0) cc_final: 0.8588 (OUTLIER) REVERT: A 331 ASP cc_start: 0.9003 (m-30) cc_final: 0.8735 (m-30) REVERT: A 724 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6883 (pp) REVERT: A 1047 LYS cc_start: 0.4578 (pptt) cc_final: 0.4306 (tmtt) REVERT: A 1099 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8537 (mm-30) REVERT: A 1156 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7964 (mmpt) REVERT: A 1325 LYS cc_start: 0.8899 (ptmm) cc_final: 0.8336 (tttp) REVERT: A 1326 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6913 (t80) outliers start: 25 outliers final: 11 residues processed: 82 average time/residue: 1.1381 time to fit residues: 102.4200 Evaluate side-chains 65 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 724 ILE 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 1116 SER Chi-restraints excluded: chain A residue 1326 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 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 = 0.3626 r_free = 0.3626 target = 0.098522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063902 restraints weight = 25718.055| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.98 r_work: 0.2765 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11930 Z= 0.129 Angle : 0.549 14.349 16627 Z= 0.277 Chirality : 0.038 0.197 1943 Planarity : 0.003 0.050 1722 Dihedral : 18.488 155.796 2799 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.74 % Allowed : 23.05 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1136 helix: 1.29 (0.23), residues: 561 sheet: 0.19 (0.50), residues: 111 loop : -0.04 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.011 0.001 PHE A 518 TYR 0.013 0.001 TYR A1242 ARG 0.013 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 510) hydrogen bonds : angle 4.23255 ( 1446) covalent geometry : bond 0.00289 (11930) covalent geometry : angle 0.54889 (16627) *********************** 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 71 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8540 (tp30) cc_final: 0.7974 (tp30) REVERT: A 202 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8856 (t0) REVERT: A 284 ASP cc_start: 0.9037 (p0) cc_final: 0.8583 (t0) REVERT: A 331 ASP cc_start: 0.9021 (m-30) cc_final: 0.8720 (m-30) REVERT: A 724 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6846 (pp) REVERT: A 1047 LYS cc_start: 0.4651 (pptt) cc_final: 0.4378 (tmtt) REVERT: A 1099 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8548 (mm-30) REVERT: A 1156 LYS cc_start: 0.8305 (mmmm) cc_final: 0.7965 (mppt) REVERT: A 1325 LYS cc_start: 0.8897 (ptmm) cc_final: 0.8329 (tttp) REVERT: A 1326 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6961 (t80) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 1.0683 time to fit residues: 80.7542 Evaluate side-chains 68 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 244 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 631 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 24 optimal weight: 0.0270 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 84 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 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 = 0.3648 r_free = 0.3648 target = 0.099787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065309 restraints weight = 25294.665| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.96 r_work: 0.2792 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11930 Z= 0.113 Angle : 0.534 14.446 16627 Z= 0.269 Chirality : 0.037 0.196 1943 Planarity : 0.003 0.047 1722 Dihedral : 18.394 155.188 2799 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.33 % Allowed : 23.36 % Favored : 75.31 % 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: 0.99 (0.26), residues: 1136 helix: 1.37 (0.23), residues: 563 sheet: 0.25 (0.50), residues: 111 loop : -0.00 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.001 PHE A 569 TYR 0.011 0.001 TYR A1242 ARG 0.012 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 510) hydrogen bonds : angle 4.17673 ( 1446) covalent geometry : bond 0.00251 (11930) covalent geometry : angle 0.53415 (16627) ********************** 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 74 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8476 (tp30) cc_final: 0.7917 (tp30) REVERT: A 202 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8859 (t0) REVERT: A 284 ASP cc_start: 0.9014 (p0) cc_final: 0.8667 (t0) REVERT: A 331 ASP cc_start: 0.9035 (m-30) cc_final: 0.8744 (m-30) REVERT: A 724 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6893 (pp) REVERT: A 1047 LYS cc_start: 0.4714 (pptt) cc_final: 0.4432 (tmtt) REVERT: A 1099 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8550 (mm-30) REVERT: A 1156 LYS cc_start: 0.8280 (mmmm) cc_final: 0.7981 (mppt) REVERT: A 1303 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7612 (mmt90) REVERT: A 1325 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8385 (tttp) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 1.0897 time to fit residues: 85.7809 Evaluate side-chains 65 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 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 963 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1269 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 3 optimal weight: 0.4980 chunk 69 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3606 r_free = 0.3606 target = 0.097439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.062655 restraints weight = 25452.541| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.96 r_work: 0.2725 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11930 Z= 0.185 Angle : 0.580 15.492 16627 Z= 0.293 Chirality : 0.039 0.217 1943 Planarity : 0.003 0.045 1722 Dihedral : 18.545 155.727 2799 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.54 % Allowed : 23.46 % Favored : 75.00 % 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: 0.87 (0.25), residues: 1136 helix: 1.30 (0.23), residues: 560 sheet: 0.23 (0.50), residues: 111 loop : -0.11 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 PHE 0.016 0.001 PHE A1105 TYR 0.014 0.001 TYR A 155 ARG 0.012 0.001 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 510) hydrogen bonds : angle 4.28961 ( 1446) covalent geometry : bond 0.00417 (11930) covalent geometry : angle 0.58006 (16627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8714.19 seconds wall clock time: 153 minutes 14.98 seconds (9194.98 seconds total)