Starting phenix.real_space_refine on Sun Nov 17 16:52:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spq_40681/11_2024/8spq_40681.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spq_40681/11_2024/8spq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spq_40681/11_2024/8spq_40681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spq_40681/11_2024/8spq_40681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spq_40681/11_2024/8spq_40681.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spq_40681/11_2024/8spq_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.50, per 1000 atoms: 0.67 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: 3.90 Conformation dependent library (CDL) restraints added in 1.4 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: 5.87 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: 8.44 Time building geometry restraints manager: 4.46 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: 3.460 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 42.080 Find NCS groups from input model: 0.140 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.210 ------------------------------------------------------------------------------- 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= 0.292 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 *********************** 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 : 1.540 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: 0.3229 time to fit residues: 38.2925 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 : 1.490 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1364 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= 0.223 Angle : 0.584 9.407 20494 Z= 0.307 Chirality : 0.039 0.202 2345 Planarity : 0.004 0.050 2076 Dihedral : 19.371 153.700 3485 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.12 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 *********************** 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 : 1.653 Fit side-chains revert: symmetry clash REVERT: A 221 ARG cc_start: 0.6972 (ttm170) cc_final: 0.6708 (ttm170) REVERT: A 296 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8441 (pp) REVERT: A 534 MET cc_start: 0.8163 (pmt) cc_final: 0.7925 (pmm) REVERT: A 781 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7916 (tmm) REVERT: A 947 ASP cc_start: 0.8008 (p0) cc_final: 0.7253 (t0) REVERT: A 1069 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8181 (p) REVERT: A 1148 LYS cc_start: 0.9148 (mptt) cc_final: 0.8783 (mmmm) REVERT: A 1242 TYR cc_start: 0.8473 (t80) cc_final: 0.8074 (t80) REVERT: A 1257 LEU cc_start: 0.9152 (mm) cc_final: 0.8938 (mm) outliers start: 29 outliers final: 10 residues processed: 93 average time/residue: 0.3178 time to fit residues: 43.0647 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 : 1.439 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2250 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= 0.200 Angle : 0.526 7.526 20494 Z= 0.279 Chirality : 0.038 0.210 2345 Planarity : 0.003 0.047 2076 Dihedral : 19.233 154.617 3485 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.56 % Allowed : 17.45 % Favored : 79.98 % 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: 0.44 (0.23), residues: 1333 helix: 0.88 (0.21), residues: 659 sheet: -0.38 (0.48), residues: 121 loop : -0.13 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 PHE 0.014 0.001 PHE A 553 TYR 0.016 0.001 TYR A1242 ARG 0.006 0.001 ARG A 765 *********************** 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 90 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 1.411 Fit side-chains REVERT: A 294 LYS cc_start: 0.9051 (tttt) cc_final: 0.8609 (ttmt) REVERT: A 307 ARG cc_start: 0.7617 (mmm160) cc_final: 0.7109 (mmm160) REVERT: A 465 MET cc_start: 0.8914 (tmm) cc_final: 0.8681 (tmm) REVERT: A 534 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7295 (ptt) REVERT: A 943 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7765 (p90) REVERT: A 947 ASP cc_start: 0.8043 (p0) cc_final: 0.7226 (t0) REVERT: A 1089 MET cc_start: 0.9369 (ttt) cc_final: 0.8739 (mtp) REVERT: A 1326 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8386 (t80) outliers start: 31 outliers final: 13 residues processed: 83 average time/residue: 0.3160 time to fit residues: 38.7286 Evaluate side-chains 69 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 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 1318 LEU Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 69 optimal weight: 0.0470 chunk 126 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 14713 Z= 0.479 Angle : 0.690 8.848 20494 Z= 0.360 Chirality : 0.044 0.199 2345 Planarity : 0.004 0.052 2076 Dihedral : 19.307 154.872 3483 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.64 % Allowed : 17.54 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1333 helix: 0.68 (0.20), residues: 657 sheet: -0.61 (0.48), residues: 116 loop : -0.34 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.010 0.002 HIS A 328 PHE 0.023 0.002 PHE A1105 TYR 0.015 0.002 TYR A 529 ARG 0.009 0.001 ARG A 535 *********************** 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 95 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 51 time to evaluate : 1.539 Fit side-chains REVERT: A 294 LYS cc_start: 0.9321 (tttt) cc_final: 0.9035 (ttpt) REVERT: A 307 ARG cc_start: 0.7730 (mmm160) cc_final: 0.7265 (mmm160) REVERT: A 534 MET cc_start: 0.8445 (pmt) cc_final: 0.7647 (ptt) REVERT: A 781 MET cc_start: 0.8482 (tmm) cc_final: 0.7883 (tmm) REVERT: A 798 GLU cc_start: 0.9023 (tp30) cc_final: 0.8675 (tp30) REVERT: A 837 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8660 (t0) REVERT: A 913 LYS cc_start: 0.8249 (tttt) cc_final: 0.7749 (ttmt) REVERT: A 943 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7725 (p90) REVERT: A 1089 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.8990 (mtp) outliers start: 44 outliers final: 20 residues processed: 87 average time/residue: 0.2993 time to fit residues: 39.0866 Evaluate side-chains 69 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 837 ASP Chi-restraints excluded: chain A residue 839 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 1039 TYR Chi-restraints excluded: chain A residue 1089 MET 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 Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14713 Z= 0.168 Angle : 0.514 6.993 20494 Z= 0.273 Chirality : 0.037 0.189 2345 Planarity : 0.003 0.047 2076 Dihedral : 19.136 153.990 3483 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.65 % Allowed : 18.78 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1333 helix: 1.15 (0.21), residues: 655 sheet: -0.47 (0.51), residues: 114 loop : -0.18 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE A1105 TYR 0.015 0.001 TYR A1242 ARG 0.007 0.000 ARG A 535 *********************** 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 78 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9089 (mt) REVERT: A 221 ARG cc_start: 0.7069 (ttm170) cc_final: 0.6529 (ttp80) REVERT: A 294 LYS cc_start: 0.9310 (tttt) cc_final: 0.9001 (ttmt) REVERT: A 307 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7264 (mmm160) REVERT: A 534 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7761 (ptt) REVERT: A 548 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9026 (mp) REVERT: A 781 MET cc_start: 0.8420 (tmm) cc_final: 0.7783 (tmm) REVERT: A 798 GLU cc_start: 0.8954 (tp30) cc_final: 0.8655 (tp30) REVERT: A 913 LYS cc_start: 0.8236 (tttt) cc_final: 0.7709 (ttmt) REVERT: A 947 ASP cc_start: 0.8281 (p0) cc_final: 0.7646 (t0) REVERT: A 1089 MET cc_start: 0.9363 (ttt) cc_final: 0.8973 (mtp) outliers start: 20 outliers final: 10 residues processed: 75 average time/residue: 0.3126 time to fit residues: 34.6810 Evaluate side-chains 66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 647 VAL 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 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER 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 47 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14713 Z= 0.265 Angle : 0.532 7.850 20494 Z= 0.282 Chirality : 0.038 0.189 2345 Planarity : 0.003 0.048 2076 Dihedral : 19.041 153.590 3483 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.73 % Allowed : 18.53 % Favored : 78.74 % 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: 0.72 (0.23), residues: 1333 helix: 1.28 (0.21), residues: 655 sheet: -0.58 (0.50), residues: 114 loop : -0.14 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.014 0.001 PHE A1105 TYR 0.012 0.001 TYR A 155 ARG 0.006 0.000 ARG A 221 *********************** 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 92 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9073 (mt) REVERT: A 221 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6646 (ttp80) REVERT: A 294 LYS cc_start: 0.9355 (tttt) cc_final: 0.9068 (ttmt) REVERT: A 307 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7338 (mmm160) REVERT: A 534 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7749 (ptt) REVERT: A 548 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9114 (mp) REVERT: A 781 MET cc_start: 0.8497 (tmm) cc_final: 0.7828 (tmm) REVERT: A 798 GLU cc_start: 0.8971 (tp30) cc_final: 0.8650 (tp30) REVERT: A 913 LYS cc_start: 0.8282 (tttt) cc_final: 0.7743 (ttmt) REVERT: A 943 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7804 (p90) REVERT: A 947 ASP cc_start: 0.8388 (p0) cc_final: 0.7749 (t0) REVERT: A 1089 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.9011 (mtp) outliers start: 33 outliers final: 19 residues processed: 84 average time/residue: 0.3161 time to fit residues: 38.8730 Evaluate side-chains 79 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 548 ILE 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14713 Z= 0.218 Angle : 0.502 7.423 20494 Z= 0.268 Chirality : 0.037 0.188 2345 Planarity : 0.003 0.047 2076 Dihedral : 18.982 153.336 3483 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.56 % Allowed : 18.11 % Favored : 79.32 % 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: 0.83 (0.23), residues: 1333 helix: 1.41 (0.21), residues: 654 sheet: -0.56 (0.51), residues: 114 loop : -0.11 (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 0.011 0.001 PHE A1105 TYR 0.013 0.001 TYR A 155 ARG 0.005 0.000 ARG A 221 *********************** 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 91 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9047 (mt) REVERT: A 294 LYS cc_start: 0.9396 (tttt) cc_final: 0.9132 (ttmt) REVERT: A 307 ARG cc_start: 0.7746 (mmm160) cc_final: 0.7310 (mmm160) REVERT: A 534 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7624 (ptt) REVERT: A 548 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9145 (mp) REVERT: A 781 MET cc_start: 0.8474 (tmm) cc_final: 0.7820 (tmm) REVERT: A 798 GLU cc_start: 0.8979 (tp30) cc_final: 0.8656 (tp30) REVERT: A 913 LYS cc_start: 0.8290 (tttt) cc_final: 0.7722 (ttmt) REVERT: A 943 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.7784 (p90) REVERT: A 947 ASP cc_start: 0.8407 (p0) cc_final: 0.7777 (t0) REVERT: A 1089 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9016 (mtp) REVERT: A 1245 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7723 (mp) outliers start: 31 outliers final: 20 residues processed: 84 average time/residue: 0.3132 time to fit residues: 38.6260 Evaluate side-chains 82 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 548 ILE Chi-restraints excluded: chain A residue 559 VAL 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 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 1089 MET 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 1287 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR 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 87 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14713 Z= 0.197 Angle : 0.496 6.860 20494 Z= 0.265 Chirality : 0.036 0.188 2345 Planarity : 0.003 0.053 2076 Dihedral : 18.903 152.913 3483 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.82 % Allowed : 19.19 % 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: 0.90 (0.23), residues: 1333 helix: 1.48 (0.21), residues: 654 sheet: -0.52 (0.51), residues: 114 loop : -0.12 (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 0.014 0.000 ARG A 221 *********************** 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 80 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.9433 (tttt) cc_final: 0.9197 (ttmt) REVERT: A 307 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7533 (mmm160) REVERT: A 534 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7679 (ptt) REVERT: A 548 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9154 (mp) REVERT: A 781 MET cc_start: 0.8489 (tmm) cc_final: 0.7827 (tmm) REVERT: A 798 GLU cc_start: 0.8980 (tp30) cc_final: 0.8657 (tp30) REVERT: A 913 LYS cc_start: 0.8309 (tttt) cc_final: 0.7732 (ttmt) REVERT: A 947 ASP cc_start: 0.8425 (p0) cc_final: 0.7760 (t0) REVERT: A 1089 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9025 (mtp) REVERT: A 1245 LEU cc_start: 0.8172 (mt) cc_final: 0.7768 (mp) outliers start: 22 outliers final: 17 residues processed: 75 average time/residue: 0.3191 time to fit residues: 35.3790 Evaluate side-chains 76 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 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 750 VAL Chi-restraints excluded: chain A residue 758 ASN 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 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER 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 134 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 40 optimal weight: 0.0170 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 0.0050 chunk 86 optimal weight: 1.9990 overall best weight: 0.5234 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4134 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= 0.142 Angle : 0.474 6.959 20494 Z= 0.254 Chirality : 0.035 0.187 2345 Planarity : 0.003 0.043 2076 Dihedral : 18.822 152.106 3483 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.82 % Allowed : 19.19 % 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: 1.01 (0.24), residues: 1333 helix: 1.58 (0.21), residues: 658 sheet: -0.30 (0.54), residues: 113 loop : -0.12 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.004 0.000 HIS A 328 PHE 0.007 0.001 PHE A1038 TYR 0.012 0.001 TYR A 155 ARG 0.002 0.000 ARG A1298 *********************** 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 87 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.9435 (tttt) cc_final: 0.9207 (ttmt) REVERT: A 307 ARG cc_start: 0.7904 (mmm160) cc_final: 0.7537 (mmm160) REVERT: A 534 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7636 (ptt) REVERT: A 781 MET cc_start: 0.8464 (tmm) cc_final: 0.7860 (tmm) REVERT: A 798 GLU cc_start: 0.8974 (tp30) cc_final: 0.8665 (tp30) REVERT: A 913 LYS cc_start: 0.8306 (tttt) cc_final: 0.7728 (ttmt) REVERT: A 947 ASP cc_start: 0.8303 (p0) cc_final: 0.7643 (t0) REVERT: A 1089 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9033 (mtp) REVERT: A 1116 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 1245 LEU cc_start: 0.8057 (mt) cc_final: 0.7641 (mp) outliers start: 22 outliers final: 14 residues processed: 82 average time/residue: 0.3151 time to fit residues: 37.7319 Evaluate side-chains 74 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 534 MET 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 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 1087 LEU Chi-restraints excluded: chain A residue 1089 MET 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 1280 VAL 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 138 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A1264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14713 Z= 0.283 Angle : 0.557 15.681 20494 Z= 0.290 Chirality : 0.038 0.189 2345 Planarity : 0.003 0.047 2076 Dihedral : 18.866 153.381 3483 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.57 % Allowed : 20.10 % Favored : 78.33 % 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: 0.85 (0.23), residues: 1333 helix: 1.44 (0.21), residues: 656 sheet: -0.41 (0.53), residues: 113 loop : -0.19 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.013 0.001 PHE A1105 TYR 0.011 0.001 TYR A 155 ARG 0.007 0.000 ARG A 221 ********************** 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: 19 poor density : 57 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8312 (ptt180) cc_final: 0.8099 (mmp-170) REVERT: A 294 LYS cc_start: 0.9464 (tttt) cc_final: 0.9225 (ttmt) REVERT: A 307 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7523 (mmm160) REVERT: A 534 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7867 (ptt) REVERT: A 781 MET cc_start: 0.8509 (tmm) cc_final: 0.7849 (tmm) REVERT: A 798 GLU cc_start: 0.8993 (tp30) cc_final: 0.8680 (tp30) REVERT: A 913 LYS cc_start: 0.8318 (tttt) cc_final: 0.7776 (ttmt) REVERT: A 947 ASP cc_start: 0.8495 (p0) cc_final: 0.7819 (t0) REVERT: A 1089 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.9040 (mtp) REVERT: A 1245 LEU cc_start: 0.8191 (mt) cc_final: 0.7797 (mp) outliers start: 19 outliers final: 16 residues processed: 72 average time/residue: 0.3351 time to fit residues: 35.9685 Evaluate side-chains 74 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 534 MET 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 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 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1280 VAL 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 123 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.076240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.054880 restraints weight = 40794.353| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.91 r_work: 0.2710 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14713 Z= 0.242 Angle : 0.536 13.194 20494 Z= 0.280 Chirality : 0.037 0.189 2345 Planarity : 0.003 0.046 2076 Dihedral : 18.876 153.325 3483 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.65 % Allowed : 19.85 % 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: 0.82 (0.23), residues: 1333 helix: 1.42 (0.21), residues: 656 sheet: -0.42 (0.53), residues: 113 loop : -0.20 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.011 0.001 PHE A1105 TYR 0.013 0.001 TYR A1242 ARG 0.015 0.000 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.26 seconds wall clock time: 50 minutes 10.28 seconds (3010.28 seconds total)