Starting phenix.real_space_refine on Thu Jun 12 18:15:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spq_40681/06_2025/8spq_40681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spq_40681/06_2025/8spq_40681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8spq_40681/06_2025/8spq_40681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spq_40681/06_2025/8spq_40681.map" model { file = "/net/cci-nas-00/data/ceres_data/8spq_40681/06_2025/8spq_40681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spq_40681/06_2025/8spq_40681.cif" } resolution = 3.26 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 148 5.49 5 Mg 4 5.21 5 S 22 5.16 5 C 8449 2.51 5 N 2490 2.21 5 O 3034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14147 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 11002 Classifications: {'peptide': 1341} Link IDs: {'PTRANS': 36, 'TRANS': 1304} Chain breaks: 3 Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2100 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "E" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.10, per 1000 atoms: 0.64 Number of scatterers: 14147 At special positions: 0 Unit cell: (87.486, 122.48, 121.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 148 15.00 Mg 4 11.99 O 3034 8.00 N 2490 7.00 C 8449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 9 sheets defined 54.0% alpha, 9.5% beta 54 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.837A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.866A 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 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 217 through 229 removed outlier: 4.816A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.747A pdb=" N LEU A 275 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 276 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 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 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.924A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.264A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.767A 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 483 through 494 removed outlier: 3.523A pdb=" N SER A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (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 572 removed outlier: 3.950A pdb=" N PHE A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.590A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.357A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 669 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 712 removed outlier: 3.983A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.024A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.799A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 804 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.908A pdb=" N LEU A 833 " --> pdb=" O ILE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 859 through 866 Processing helix chain 'A' and resid 872 through 888 removed outlier: 5.695A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 removed outlier: 3.550A pdb=" N GLY A 906 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.505A pdb=" N LYS A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 940 removed outlier: 3.792A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.588A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.659A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1043 removed outlier: 4.253A pdb=" N MET A1043 " --> pdb=" O TYR A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1047 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 Processing helix chain 'A' and resid 1177 through 1185 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 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.675A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.570A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) 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 959 removed outlier: 6.322A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.508A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.513A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.673A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 134 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 8.10 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3515 1.34 - 1.46: 3584 1.46 - 1.58: 7278 1.58 - 1.70: 294 1.70 - 1.82: 42 Bond restraints: 14713 Sorted by residual: bond pdb=" CB ASN A 946 " pdb=" CG ASN A 946 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.58e+00 bond pdb=" CB LYS A 4 " pdb=" CG LYS A 4 " ideal model delta sigma weight residual 1.520 1.581 -0.061 3.00e-02 1.11e+03 4.14e+00 bond pdb=" CB LYS A1031 " pdb=" CG LYS A1031 " ideal model delta sigma weight residual 1.520 1.581 -0.061 3.00e-02 1.11e+03 4.08e+00 bond pdb=" CB ASP A1299 " pdb=" CG ASP A1299 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" CB ASP A 585 " pdb=" CG ASP A 585 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.58e+00 ... (remaining 14708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 20215 3.42 - 6.83: 219 6.83 - 10.25: 52 10.25 - 13.67: 6 13.67 - 17.08: 2 Bond angle restraints: 20494 Sorted by residual: angle pdb=" CA LYS A 877 " pdb=" CB LYS A 877 " pdb=" CG LYS A 877 " ideal model delta sigma weight residual 114.10 124.76 -10.66 2.00e+00 2.50e-01 2.84e+01 angle pdb=" CA LYS A 183 " pdb=" CB LYS A 183 " pdb=" CG LYS A 183 " ideal model delta sigma weight residual 114.10 124.63 -10.53 2.00e+00 2.50e-01 2.77e+01 angle pdb=" CA LYS A1255 " pdb=" CB LYS A1255 " pdb=" CG LYS A1255 " ideal model delta sigma weight residual 114.10 124.44 -10.34 2.00e+00 2.50e-01 2.68e+01 angle pdb=" CA LYS A 4 " pdb=" CB LYS A 4 " pdb=" CG LYS A 4 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" CB LYS A1031 " pdb=" CG LYS A1031 " pdb=" CD LYS A1031 " ideal model delta sigma weight residual 111.30 122.85 -11.55 2.30e+00 1.89e-01 2.52e+01 ... (remaining 20489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.45: 8101 29.45 - 58.90: 690 58.90 - 88.35: 117 88.35 - 117.80: 3 117.80 - 147.25: 2 Dihedral angle restraints: 8913 sinusoidal: 4969 harmonic: 3944 Sorted by residual: dihedral pdb=" CA PRO A 871 " pdb=" C PRO A 871 " pdb=" N SER A 872 " pdb=" CA SER A 872 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ASN A 869 " pdb=" C ASN A 869 " pdb=" N VAL A 870 " pdb=" CA VAL A 870 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU A 444 " pdb=" C LEU A 444 " pdb=" N THR A 445 " pdb=" CA THR A 445 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 8910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2198 0.096 - 0.191: 137 0.191 - 0.287: 8 0.287 - 0.382: 1 0.382 - 0.478: 1 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CG LEU A 158 " pdb=" CB LEU A 158 " pdb=" CD1 LEU A 158 " pdb=" CD2 LEU A 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CG LEU A 444 " pdb=" CB LEU A 444 " pdb=" CD1 LEU A 444 " pdb=" CD2 LEU A 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.13e+00 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 -2.20 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2342 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 1 " -0.028 2.00e-02 2.50e+03 1.27e-02 4.83e+00 pdb=" N9 G B 1 " 0.033 2.00e-02 2.50e+03 pdb=" C8 G B 1 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 1 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G B 1 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B 1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 1 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B 1 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 1 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 1 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 905 " -0.179 9.50e-02 1.11e+02 8.08e-02 4.81e+00 pdb=" NE ARG A 905 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 905 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 905 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 905 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1150 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C GLU A1150 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A1150 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A1151 " -0.012 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 172 2.61 - 3.18: 11299 3.18 - 3.75: 24400 3.75 - 4.33: 32013 4.33 - 4.90: 49785 Nonbonded interactions: 117669 Sorted by model distance: nonbonded pdb=" OP2 DC D 34 " pdb="MG MG A1402 " model vdw 2.037 2.170 nonbonded pdb=" OP1 DC D 34 " pdb="MG MG A1401 " model vdw 2.061 2.170 nonbonded pdb=" OE1 GLN A 402 " pdb=" O2' U B 44 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP A 672 " pdb=" OG1 THR A 703 " model vdw 2.258 3.040 nonbonded pdb=" OP3 DT E 0 " pdb="MG MG A1403 " model vdw 2.293 2.170 ... (remaining 117664 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: 3.320 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 40.520 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 0.072 14713 Z= 0.204 Angle : 0.945 17.081 20494 Z= 0.478 Chirality : 0.048 0.478 2345 Planarity : 0.006 0.081 2076 Dihedral : 19.589 147.255 6359 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.33 % Allowed : 24.07 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1333 helix: -0.88 (0.18), residues: 628 sheet: -0.64 (0.46), residues: 131 loop : -0.62 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 883 HIS 0.017 0.001 HIS A 137 PHE 0.024 0.002 PHE A 553 TYR 0.031 0.002 TYR A1294 ARG 0.016 0.002 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.15037 ( 629) hydrogen bonds : angle 6.39911 ( 1731) covalent geometry : bond 0.00465 (14713) covalent geometry : angle 0.94472 (20494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7666 (t0) cc_final: 0.7390 (p0) REVERT: A 221 ARG cc_start: 0.6813 (ttm170) cc_final: 0.6339 (ttp80) REVERT: A 516 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8834 (mt-10) REVERT: A 947 ASP cc_start: 0.7711 (p0) cc_final: 0.7024 (t0) REVERT: A 1148 LYS cc_start: 0.9172 (mptt) cc_final: 0.8794 (mmmm) outliers start: 4 outliers final: 1 residues processed: 83 average time/residue: 0.3358 time to fit residues: 39.9551 Evaluate side-chains 66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1302 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN A 807 GLN A1256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.082630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061026 restraints weight = 39951.935| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.09 r_work: 0.2858 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14713 Z= 0.159 Angle : 0.584 9.413 20494 Z= 0.307 Chirality : 0.039 0.202 2345 Planarity : 0.004 0.050 2076 Dihedral : 19.371 153.696 3485 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.40 % Allowed : 18.53 % Favored : 79.07 % 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: -0.08 (0.23), residues: 1333 helix: 0.36 (0.20), residues: 644 sheet: -0.42 (0.49), residues: 123 loop : -0.29 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 883 HIS 0.005 0.001 HIS A 137 PHE 0.010 0.001 PHE A1105 TYR 0.013 0.001 TYR A1242 ARG 0.006 0.001 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 629) hydrogen bonds : angle 4.64130 ( 1731) covalent geometry : bond 0.00353 (14713) covalent geometry : angle 0.58423 (20494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 221 ARG cc_start: 0.6903 (ttm170) cc_final: 0.6647 (ttm170) REVERT: A 296 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8425 (pp) REVERT: A 534 MET cc_start: 0.8185 (pmt) cc_final: 0.7964 (pmm) REVERT: A 781 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7915 (tmm) REVERT: A 947 ASP cc_start: 0.7938 (p0) cc_final: 0.7180 (t0) REVERT: A 1069 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 1148 LYS cc_start: 0.9096 (mptt) cc_final: 0.8730 (mmmm) REVERT: A 1242 TYR cc_start: 0.8567 (t80) cc_final: 0.8177 (t80) REVERT: A 1257 LEU cc_start: 0.9112 (mm) cc_final: 0.8910 (mm) outliers start: 29 outliers final: 10 residues processed: 93 average time/residue: 0.2815 time to fit residues: 38.4653 Evaluate side-chains 71 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057787 restraints weight = 40701.977| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.97 r_work: 0.2766 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14713 Z= 0.173 Angle : 0.550 8.114 20494 Z= 0.292 Chirality : 0.039 0.199 2345 Planarity : 0.004 0.048 2076 Dihedral : 19.287 154.885 3485 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.65 % Allowed : 17.54 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1333 helix: 0.80 (0.21), residues: 658 sheet: -0.40 (0.48), residues: 121 loop : -0.18 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.015 0.001 PHE A 553 TYR 0.015 0.001 TYR A1242 ARG 0.005 0.001 ARG A1337 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 629) hydrogen bonds : angle 4.36522 ( 1731) covalent geometry : bond 0.00385 (14713) covalent geometry : angle 0.55047 (20494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 1.432 Fit side-chains REVERT: A 294 LYS cc_start: 0.9164 (tttt) cc_final: 0.8662 (ttmt) REVERT: A 307 ARG cc_start: 0.7555 (mmm160) cc_final: 0.7018 (mmm160) REVERT: A 465 MET cc_start: 0.8912 (tmm) cc_final: 0.8690 (tmm) REVERT: A 534 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7279 (ptt) REVERT: A 781 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7706 (tmm) REVERT: A 943 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7700 (p90) REVERT: A 947 ASP cc_start: 0.8053 (p0) cc_final: 0.7235 (t0) REVERT: A 1089 MET cc_start: 0.9307 (ttt) cc_final: 0.8723 (mtp) REVERT: A 1326 TYR cc_start: 0.8731 (t80) cc_final: 0.8453 (t80) outliers start: 32 outliers final: 14 residues processed: 86 average time/residue: 0.3003 time to fit residues: 37.9087 Evaluate side-chains 70 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 137 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.074879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.053295 restraints weight = 41184.505| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.95 r_work: 0.2661 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 14713 Z= 0.310 Angle : 0.654 11.661 20494 Z= 0.340 Chirality : 0.043 0.196 2345 Planarity : 0.004 0.053 2076 Dihedral : 19.250 154.681 3485 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.06 % Allowed : 17.95 % Favored : 78.99 % 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: 0.24 (0.23), residues: 1333 helix: 0.81 (0.20), residues: 655 sheet: -0.48 (0.47), residues: 120 loop : -0.34 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.019 0.002 PHE A1105 TYR 0.013 0.002 TYR A1294 ARG 0.009 0.001 ARG A 535 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 629) hydrogen bonds : angle 4.53153 ( 1731) covalent geometry : bond 0.00690 (14713) covalent geometry : angle 0.65368 (20494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 56 time to evaluate : 1.597 Fit side-chains REVERT: A 294 LYS cc_start: 0.9342 (tttt) cc_final: 0.8939 (ttmt) REVERT: A 307 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7168 (mmm160) REVERT: A 534 MET cc_start: 0.8447 (pmt) cc_final: 0.7464 (ptt) REVERT: A 781 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7798 (tmm) REVERT: A 798 GLU cc_start: 0.9054 (tp30) cc_final: 0.8751 (tp30) REVERT: A 837 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8605 (t0) REVERT: A 913 LYS cc_start: 0.8271 (tttt) cc_final: 0.7778 (ttmt) REVERT: A 943 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7610 (p90) REVERT: A 1089 MET cc_start: 0.9357 (ttt) cc_final: 0.8958 (mtp) outliers start: 37 outliers final: 19 residues processed: 86 average time/residue: 0.2928 time to fit residues: 37.7768 Evaluate side-chains 72 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.077902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.056301 restraints weight = 40776.092| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.96 r_work: 0.2733 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14713 Z= 0.122 Angle : 0.503 7.472 20494 Z= 0.268 Chirality : 0.037 0.188 2345 Planarity : 0.003 0.045 2076 Dihedral : 19.103 153.739 3485 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.32 % Allowed : 18.44 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1333 helix: 1.18 (0.21), residues: 655 sheet: -0.50 (0.49), residues: 119 loop : -0.21 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 PHE 0.011 0.001 PHE A1105 TYR 0.015 0.001 TYR A1242 ARG 0.004 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 629) hydrogen bonds : angle 4.25562 ( 1731) covalent geometry : bond 0.00266 (14713) covalent geometry : angle 0.50291 (20494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 221 ARG cc_start: 0.6900 (ttm170) cc_final: 0.6358 (ttp80) REVERT: A 294 LYS cc_start: 0.9333 (tttt) cc_final: 0.8916 (ttpt) REVERT: A 307 ARG cc_start: 0.7720 (mmm160) cc_final: 0.7219 (mmm160) REVERT: A 534 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7576 (ptt) REVERT: A 586 ARG cc_start: 0.8699 (ttm-80) cc_final: 0.8349 (ttm-80) REVERT: A 781 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7792 (tmm) REVERT: A 798 GLU cc_start: 0.9065 (tp30) cc_final: 0.8741 (tp30) REVERT: A 913 LYS cc_start: 0.8290 (tttt) cc_final: 0.7744 (ttmt) REVERT: A 947 ASP cc_start: 0.8119 (p0) cc_final: 0.7462 (t0) REVERT: A 1089 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8963 (mtp) outliers start: 28 outliers final: 13 residues processed: 80 average time/residue: 0.3351 time to fit residues: 39.1714 Evaluate side-chains 70 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 5 optimal weight: 0.2980 chunk 126 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.077519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056089 restraints weight = 41011.256| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.92 r_work: 0.2725 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14713 Z= 0.141 Angle : 0.506 7.938 20494 Z= 0.267 Chirality : 0.037 0.188 2345 Planarity : 0.003 0.046 2076 Dihedral : 19.020 153.129 3485 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.23 % Allowed : 18.69 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1333 helix: 1.32 (0.21), residues: 655 sheet: -0.57 (0.48), residues: 119 loop : -0.18 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A1105 TYR 0.012 0.001 TYR A1242 ARG 0.004 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 629) hydrogen bonds : angle 4.20604 ( 1731) covalent geometry : bond 0.00313 (14713) covalent geometry : angle 0.50622 (20494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 2.828 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9071 (mt) REVERT: A 221 ARG cc_start: 0.6939 (ttm170) cc_final: 0.6398 (ttp80) REVERT: A 294 LYS cc_start: 0.9352 (tttt) cc_final: 0.8942 (ttpt) REVERT: A 307 ARG cc_start: 0.7720 (mmm160) cc_final: 0.7278 (mmm160) REVERT: A 534 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7622 (ptt) REVERT: A 586 ARG cc_start: 0.8699 (ttm-80) cc_final: 0.8356 (ttm-80) REVERT: A 629 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8287 (mmm160) REVERT: A 781 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7815 (tmm) REVERT: A 798 GLU cc_start: 0.9091 (tp30) cc_final: 0.8763 (tp30) REVERT: A 913 LYS cc_start: 0.8295 (tttt) cc_final: 0.7743 (ttmt) REVERT: A 947 ASP cc_start: 0.8150 (p0) cc_final: 0.7506 (t0) REVERT: A 1245 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7604 (mp) outliers start: 27 outliers final: 16 residues processed: 80 average time/residue: 0.3620 time to fit residues: 43.6247 Evaluate side-chains 74 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 20 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.054244 restraints weight = 41324.068| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.95 r_work: 0.2682 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14713 Z= 0.210 Angle : 0.555 8.382 20494 Z= 0.291 Chirality : 0.039 0.190 2345 Planarity : 0.003 0.049 2076 Dihedral : 19.050 154.086 3485 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.06 % Allowed : 18.03 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1333 helix: 1.30 (0.21), residues: 655 sheet: -0.42 (0.51), residues: 113 loop : -0.23 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.014 0.001 PHE A1105 TYR 0.013 0.001 TYR A 155 ARG 0.005 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 629) hydrogen bonds : angle 4.28218 ( 1731) covalent geometry : bond 0.00466 (14713) covalent geometry : angle 0.55526 (20494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9059 (mt) REVERT: A 221 ARG cc_start: 0.7048 (ttm170) cc_final: 0.6821 (ttp80) REVERT: A 294 LYS cc_start: 0.9406 (tttt) cc_final: 0.9085 (ttmt) REVERT: A 307 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7313 (mmm160) REVERT: A 534 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7626 (ptt) REVERT: A 535 ARG cc_start: 0.7664 (mmp80) cc_final: 0.7441 (mmp80) REVERT: A 548 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9118 (mp) REVERT: A 781 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7835 (tmm) REVERT: A 798 GLU cc_start: 0.9096 (tp30) cc_final: 0.8762 (tp30) REVERT: A 913 LYS cc_start: 0.8350 (tttt) cc_final: 0.7790 (ttmt) REVERT: A 943 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7718 (p90) REVERT: A 947 ASP cc_start: 0.8323 (p0) cc_final: 0.7643 (t0) REVERT: A 1245 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7651 (mp) outliers start: 37 outliers final: 24 residues processed: 86 average time/residue: 0.3508 time to fit residues: 44.1790 Evaluate side-chains 85 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 142 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.054597 restraints weight = 40981.608| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.92 r_work: 0.2696 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14713 Z= 0.185 Angle : 0.527 7.642 20494 Z= 0.279 Chirality : 0.038 0.190 2345 Planarity : 0.003 0.047 2076 Dihedral : 18.994 153.659 3485 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.07 % Allowed : 18.86 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1333 helix: 1.36 (0.21), residues: 654 sheet: -0.53 (0.51), residues: 114 loop : -0.17 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.012 0.001 PHE A1105 TYR 0.013 0.001 TYR A 155 ARG 0.005 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 629) hydrogen bonds : angle 4.24184 ( 1731) covalent geometry : bond 0.00412 (14713) covalent geometry : angle 0.52725 (20494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ARG cc_start: 0.7403 (ttm170) cc_final: 0.6762 (ttp80) REVERT: A 294 LYS cc_start: 0.9468 (tttt) cc_final: 0.9201 (ttmt) REVERT: A 307 ARG cc_start: 0.7819 (mmm160) cc_final: 0.7285 (mmm160) REVERT: A 534 MET cc_start: 0.8467 (pmt) cc_final: 0.7615 (ptt) REVERT: A 535 ARG cc_start: 0.7809 (mmp80) cc_final: 0.7493 (mmp80) REVERT: A 548 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9150 (mp) REVERT: A 781 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7823 (tmm) REVERT: A 798 GLU cc_start: 0.9109 (tp30) cc_final: 0.8778 (tp30) REVERT: A 913 LYS cc_start: 0.8355 (tttt) cc_final: 0.7805 (ttmt) REVERT: A 947 ASP cc_start: 0.8303 (p0) cc_final: 0.7577 (t0) REVERT: A 1089 MET cc_start: 0.9212 (mtp) cc_final: 0.8811 (mtp) REVERT: A 1245 LEU cc_start: 0.8118 (mt) cc_final: 0.7684 (mp) outliers start: 25 outliers final: 22 residues processed: 79 average time/residue: 0.6102 time to fit residues: 74.0625 Evaluate side-chains 80 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 102 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 131 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.077981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056683 restraints weight = 40647.953| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.93 r_work: 0.2747 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14713 Z= 0.112 Angle : 0.486 7.519 20494 Z= 0.258 Chirality : 0.036 0.188 2345 Planarity : 0.003 0.044 2076 Dihedral : 18.904 152.385 3483 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.90 % Allowed : 19.11 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1333 helix: 1.49 (0.21), residues: 658 sheet: -0.49 (0.51), residues: 116 loop : -0.13 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 PHE 0.008 0.001 PHE A1105 TYR 0.014 0.001 TYR A 155 ARG 0.006 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 629) hydrogen bonds : angle 4.12915 ( 1731) covalent geometry : bond 0.00244 (14713) covalent geometry : angle 0.48590 (20494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9053 (mt) REVERT: A 221 ARG cc_start: 0.7407 (ttm170) cc_final: 0.6990 (ttp80) REVERT: A 294 LYS cc_start: 0.9467 (tttt) cc_final: 0.9199 (ttmt) REVERT: A 307 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7424 (mmm160) REVERT: A 534 MET cc_start: 0.8399 (pmt) cc_final: 0.7455 (ptt) REVERT: A 535 ARG cc_start: 0.7919 (mmp80) cc_final: 0.7544 (mmp80) REVERT: A 548 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9206 (mp) REVERT: A 781 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7805 (tmm) REVERT: A 798 GLU cc_start: 0.9102 (tp30) cc_final: 0.8776 (tp30) REVERT: A 913 LYS cc_start: 0.8381 (tttt) cc_final: 0.7787 (ttmt) REVERT: A 947 ASP cc_start: 0.8151 (p0) cc_final: 0.7497 (t0) REVERT: A 1089 MET cc_start: 0.9145 (mtp) cc_final: 0.8898 (mtp) REVERT: A 1245 LEU cc_start: 0.8073 (mt) cc_final: 0.7644 (mp) outliers start: 23 outliers final: 16 residues processed: 83 average time/residue: 0.3110 time to fit residues: 37.3564 Evaluate side-chains 75 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.0020 chunk 134 optimal weight: 5.9990 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.055633 restraints weight = 41016.839| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.93 r_work: 0.2722 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14713 Z= 0.152 Angle : 0.527 15.591 20494 Z= 0.272 Chirality : 0.037 0.188 2345 Planarity : 0.003 0.045 2076 Dihedral : 18.877 152.791 3483 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.49 % Allowed : 19.85 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1333 helix: 1.47 (0.21), residues: 654 sheet: -0.51 (0.51), residues: 114 loop : -0.13 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A1105 TYR 0.012 0.001 TYR A 155 ARG 0.006 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 629) hydrogen bonds : angle 4.14049 ( 1731) covalent geometry : bond 0.00339 (14713) covalent geometry : angle 0.52706 (20494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9043 (mt) REVERT: A 215 ARG cc_start: 0.8231 (ptt180) cc_final: 0.8031 (mmp-170) REVERT: A 221 ARG cc_start: 0.7420 (ttm170) cc_final: 0.6987 (ttp80) REVERT: A 294 LYS cc_start: 0.9486 (tttt) cc_final: 0.9216 (ttmt) REVERT: A 307 ARG cc_start: 0.7801 (mmm160) cc_final: 0.7476 (mmm160) REVERT: A 534 MET cc_start: 0.8462 (pmt) cc_final: 0.7901 (ptt) REVERT: A 548 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9170 (mp) REVERT: A 781 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7791 (tmm) REVERT: A 798 GLU cc_start: 0.9089 (tp30) cc_final: 0.8754 (tp30) REVERT: A 913 LYS cc_start: 0.8363 (tttt) cc_final: 0.7777 (ttmt) REVERT: A 947 ASP cc_start: 0.8302 (p0) cc_final: 0.7582 (t0) REVERT: A 1089 MET cc_start: 0.9206 (mtp) cc_final: 0.8940 (mtp) REVERT: A 1245 LEU cc_start: 0.8113 (mt) cc_final: 0.7657 (mp) outliers start: 18 outliers final: 15 residues processed: 73 average time/residue: 0.2880 time to fit residues: 31.9841 Evaluate side-chains 75 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 144 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.077729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.056449 restraints weight = 41038.188| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.93 r_work: 0.2744 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14713 Z= 0.125 Angle : 0.506 13.371 20494 Z= 0.263 Chirality : 0.036 0.188 2345 Planarity : 0.003 0.044 2076 Dihedral : 18.835 152.534 3483 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.90 % Allowed : 19.60 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1333 helix: 1.49 (0.21), residues: 658 sheet: -0.34 (0.53), residues: 113 loop : -0.16 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.009 0.001 PHE A1105 TYR 0.012 0.001 TYR A 155 ARG 0.005 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 629) hydrogen bonds : angle 4.10222 ( 1731) covalent geometry : bond 0.00276 (14713) covalent geometry : angle 0.50620 (20494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6171.21 seconds wall clock time: 112 minutes 13.84 seconds (6733.84 seconds total)