Starting phenix.real_space_refine on Tue May 13 18:34:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewz_50027/05_2025/9ewz_50027.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewz_50027/05_2025/9ewz_50027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ewz_50027/05_2025/9ewz_50027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewz_50027/05_2025/9ewz_50027.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewz_50027/05_2025/9ewz_50027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewz_50027/05_2025/9ewz_50027.cif" } resolution = 2.22 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= 0.004 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 50 5.49 5 Mg 1 5.21 5 S 43 5.16 5 C 6697 2.51 5 N 1853 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10780 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 9728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9728 Classifications: {'peptide': 1205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1164} Chain: "B" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 522 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 502 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 7.30, per 1000 atoms: 0.68 Number of scatterers: 10780 At special positions: 0 Unit cell: (78.44, 110.26, 129.5, 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 43 16.00 P 50 15.00 Mg 1 11.99 O 2136 8.00 N 1853 7.00 C 6697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.3 seconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 5 sheets defined 58.5% alpha, 6.6% beta 24 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'C' and resid 3 through 28 Proline residue: C 11 - end of helix Processing helix chain 'C' and resid 61 through 75 removed outlier: 3.560A pdb=" N GLU C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 101 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 137 through 148 removed outlier: 3.727A pdb=" N LEU C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY C 148 " --> pdb=" O MET C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 168 removed outlier: 3.588A pdb=" N LEU C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.508A pdb=" N LEU C 185 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 203 removed outlier: 4.398A pdb=" N GLY C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.530A pdb=" N TRP C 208 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 209 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLN C 210 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 4.020A pdb=" N GLY C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 235 through 243 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 248 through 258 removed outlier: 3.522A pdb=" N ASN C 258 " --> pdb=" O TYR C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 268 removed outlier: 3.803A pdb=" N THR C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.822A pdb=" N ILE C 307 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 335 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 340 through 349 removed outlier: 3.504A pdb=" N LEU C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 375 removed outlier: 3.870A pdb=" N ASP C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 405 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.715A pdb=" N HIS C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 removed outlier: 4.163A pdb=" N ALA C 424 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 removed outlier: 3.664A pdb=" N LEU C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 451 through 453 No H-bonds generated for 'chain 'C' and resid 451 through 453' Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 459 through 474 Processing helix chain 'C' and resid 478 through 500 Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 518 through 529 Processing helix chain 'C' and resid 535 through 545 removed outlier: 4.142A pdb=" N PHE C 545 " --> pdb=" O MET C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 565 removed outlier: 3.911A pdb=" N PHE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 579 removed outlier: 3.663A pdb=" N ASN C 578 " --> pdb=" O TRP C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 636 Processing helix chain 'C' and resid 646 through 651 Processing helix chain 'C' and resid 662 through 671 removed outlier: 3.578A pdb=" N LYS C 671 " --> pdb=" O ASN C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 677 No H-bonds generated for 'chain 'C' and resid 675 through 677' Processing helix chain 'C' and resid 688 through 692 Processing helix chain 'C' and resid 697 through 699 No H-bonds generated for 'chain 'C' and resid 697 through 699' Processing helix chain 'C' and resid 700 through 704 removed outlier: 3.541A pdb=" N SER C 703 " --> pdb=" O SER C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 746 Processing helix chain 'C' and resid 752 through 756 Processing helix chain 'C' and resid 784 through 786 No H-bonds generated for 'chain 'C' and resid 784 through 786' Processing helix chain 'C' and resid 798 through 807 Processing helix chain 'C' and resid 808 through 819 Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 838 through 856 removed outlier: 4.124A pdb=" N ASP C 842 " --> pdb=" O ASN C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 872 removed outlier: 3.693A pdb=" N GLU C 871 " --> pdb=" O LYS C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 875 through 910 removed outlier: 3.586A pdb=" N ILE C 908 " --> pdb=" O ILE C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 933 Processing helix chain 'C' and resid 941 through 962 Processing helix chain 'C' and resid 981 through 989 Processing helix chain 'C' and resid 1013 through 1027 Processing helix chain 'C' and resid 1030 through 1046 removed outlier: 4.042A pdb=" N TYR C1045 " --> pdb=" O SER C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1066 Processing helix chain 'C' and resid 1066 through 1076 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1104 through 1135 removed outlier: 4.530A pdb=" N VAL C1115 " --> pdb=" O THR C1111 " (cutoff:3.500A) Proline residue: C1116 - end of helix removed outlier: 3.627A pdb=" N ASP C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C1131 " --> pdb=" O ARG C1127 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C1134 " --> pdb=" O ASP C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1170 removed outlier: 4.341A pdb=" N ARG C1142 " --> pdb=" O GLY C1138 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU C1143 " --> pdb=" O GLU C1139 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C1148 " --> pdb=" O LYS C1144 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C1149 " --> pdb=" O ARG C1145 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET C1170 " --> pdb=" O HIS C1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 1175 through 1178 Processing helix chain 'C' and resid 1179 through 1184 Processing helix chain 'C' and resid 1193 through 1199 Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 46 removed outlier: 3.593A pdb=" N PHE C 55 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 387 through 389 removed outlier: 8.280A pdb=" N VAL C 388 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY C 352 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL C 309 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU C 353 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP C 311 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP C 503 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA C 555 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 505 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL C 557 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA C 507 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N MET C 559 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR C 602 " --> pdb=" O HIS C 586 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS C 586 " --> pdb=" O THR C 602 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 604 " --> pdb=" O MET C 584 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N MET C 584 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C 606 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 618 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 679 through 680 Processing sheet with id=AA4, first strand: chain 'C' and resid 693 through 695 removed outlier: 4.368A pdb=" N TYR C 732 " --> pdb=" O ILE C 717 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1001 through 1003 459 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2891 1.33 - 1.45: 2251 1.45 - 1.57: 5804 1.57 - 1.69: 98 1.69 - 1.81: 75 Bond restraints: 11119 Sorted by residual: bond pdb=" C2 SAM C1302 " pdb=" N3 SAM C1302 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" C8 SAM C1302 " pdb=" N7 SAM C1302 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C2 SAM C1302 " pdb=" N1 SAM C1302 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" C6 SAM C1302 " pdb=" N1 SAM C1302 " ideal model delta sigma weight residual 1.337 1.378 -0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C3' DC B 3 " pdb=" O3' DC B 3 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.90e+00 ... (remaining 11114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 15057 1.77 - 3.55: 164 3.55 - 5.32: 23 5.32 - 7.10: 5 7.10 - 8.87: 3 Bond angle restraints: 15252 Sorted by residual: angle pdb=" C LYS C 725 " pdb=" N TRP C 726 " pdb=" CA TRP C 726 " ideal model delta sigma weight residual 121.54 127.39 -5.85 1.91e+00 2.74e-01 9.39e+00 angle pdb=" O SAM C1302 " pdb=" C SAM C1302 " pdb=" OXT SAM C1302 " ideal model delta sigma weight residual 126.77 117.90 8.87 3.00e+00 1.11e-01 8.74e+00 angle pdb=" CA TYR C 86 " pdb=" CB TYR C 86 " pdb=" CG TYR C 86 " ideal model delta sigma weight residual 113.90 119.16 -5.26 1.80e+00 3.09e-01 8.53e+00 angle pdb=" N1 SAM C1302 " pdb=" C2 SAM C1302 " pdb=" N3 SAM C1302 " ideal model delta sigma weight residual 128.51 120.12 8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" C2 SAM C1302 " pdb=" N3 SAM C1302 " pdb=" C4 SAM C1302 " ideal model delta sigma weight residual 112.25 120.28 -8.03 3.00e+00 1.11e-01 7.17e+00 ... (remaining 15247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 6277 34.06 - 68.12: 264 68.12 - 102.18: 4 102.18 - 136.23: 0 136.23 - 170.29: 4 Dihedral angle restraints: 6549 sinusoidal: 3023 harmonic: 3526 Sorted by residual: dihedral pdb=" C4' DC A 14 " pdb=" C3' DC A 14 " pdb=" O3' DC A 14 " pdb=" P DC A 15 " ideal model delta sinusoidal sigma weight residual 220.00 49.71 170.29 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC B 3 " pdb=" C3' DC B 3 " pdb=" O3' DC B 3 " pdb=" P DA B 4 " ideal model delta sinusoidal sigma weight residual 220.00 50.83 169.17 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA B 16 " pdb=" C3' DA B 16 " pdb=" O3' DA B 16 " pdb=" P DG B 17 " ideal model delta sinusoidal sigma weight residual 220.00 63.06 156.94 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 6546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1166 0.034 - 0.068: 356 0.068 - 0.101: 87 0.101 - 0.135: 38 0.135 - 0.169: 3 Chirality restraints: 1650 Sorted by residual: chirality pdb=" C2' SAM C1302 " pdb=" C1' SAM C1302 " pdb=" C3' SAM C1302 " pdb=" O2' SAM C1302 " both_signs ideal model delta sigma weight residual False -2.76 -2.59 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA TRP C 696 " pdb=" N TRP C 696 " pdb=" C TRP C 696 " pdb=" CB TRP C 696 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA TYR C 86 " pdb=" N TYR C 86 " pdb=" C TYR C 86 " pdb=" CB TYR C 86 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1647 not shown) Planarity restraints: 1801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 217 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C LEU C 217 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU C 217 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR C 218 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 86 " 0.010 2.00e-02 2.50e+03 9.27e-03 1.72e+00 pdb=" CG TYR C 86 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 86 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 86 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 86 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 86 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 86 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 466 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C PHE C 466 " -0.022 2.00e-02 2.50e+03 pdb=" O PHE C 466 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU C 467 " 0.007 2.00e-02 2.50e+03 ... (remaining 1798 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 581 2.73 - 3.27: 10337 3.27 - 3.82: 17923 3.82 - 4.36: 22391 4.36 - 4.90: 36579 Nonbonded interactions: 87811 Sorted by model distance: nonbonded pdb=" OD2 ASP C 997 " pdb="MG MG C1301 " model vdw 2.190 2.170 nonbonded pdb=" OE1 GLU C1008 " pdb=" OG SER C1016 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C1054 " pdb=" OE1 GLU C1057 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP C 999 " pdb="MG MG C1301 " model vdw 2.266 2.170 nonbonded pdb=" O HIS C 318 " pdb=" OG1 THR C 321 " model vdw 2.302 3.040 ... (remaining 87806 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=1.00 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: 6.200 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 32.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 0.003 0.056 11119 Z= 0.125 Angle : 0.497 8.869 15252 Z= 0.263 Chirality : 0.038 0.169 1650 Planarity : 0.003 0.029 1801 Dihedral : 15.886 170.292 4279 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.29 % Allowed : 2.99 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1203 helix: 1.65 (0.23), residues: 578 sheet: -0.29 (0.66), residues: 67 loop : -0.61 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 PHE 0.010 0.001 PHE C 537 TYR 0.023 0.001 TYR C 86 ARG 0.002 0.000 ARG C 744 Details of bonding type rmsd hydrogen bonds : bond 0.15677 ( 519) hydrogen bonds : angle 5.77107 ( 1419) covalent geometry : bond 0.00264 (11119) covalent geometry : angle 0.49703 (15252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 1.239 Fit side-chains REVERT: C 377 ARG cc_start: 0.8183 (tpp-160) cc_final: 0.7745 (tpp-160) REVERT: C 434 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7844 (mmtp) REVERT: C 437 MET cc_start: 0.7947 (mmm) cc_final: 0.7652 (mmm) REVERT: C 469 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7368 (mtt180) REVERT: C 479 ILE cc_start: 0.8505 (mm) cc_final: 0.7886 (mm) REVERT: C 517 MET cc_start: 0.9115 (mtp) cc_final: 0.8896 (mtm) REVERT: C 1148 ASP cc_start: 0.8109 (m-30) cc_final: 0.7805 (p0) outliers start: 3 outliers final: 2 residues processed: 93 average time/residue: 1.7473 time to fit residues: 172.4806 Evaluate side-chains 66 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 801 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.061998 restraints weight = 17156.055| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.35 r_work: 0.2705 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11119 Z= 0.164 Angle : 0.561 8.477 15252 Z= 0.305 Chirality : 0.040 0.167 1650 Planarity : 0.003 0.033 1801 Dihedral : 20.186 170.008 1903 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.35 % Allowed : 5.68 % Favored : 92.97 % 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: 1.18 (0.25), residues: 1203 helix: 2.14 (0.22), residues: 580 sheet: -0.03 (0.61), residues: 79 loop : -0.59 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 862 HIS 0.003 0.001 HIS C 976 PHE 0.013 0.002 PHE C 537 TYR 0.023 0.001 TYR C 86 ARG 0.003 0.000 ARG C1165 Details of bonding type rmsd hydrogen bonds : bond 0.05805 ( 519) hydrogen bonds : angle 4.19488 ( 1419) covalent geometry : bond 0.00376 (11119) covalent geometry : angle 0.56128 (15252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8383 (pt0) REVERT: C 394 LYS cc_start: 0.7891 (tppt) cc_final: 0.7314 (mmpt) REVERT: C 417 ASP cc_start: 0.5886 (p0) cc_final: 0.4528 (p0) REVERT: C 432 GLU cc_start: 0.7521 (pm20) cc_final: 0.6553 (pm20) REVERT: C 437 MET cc_start: 0.8259 (mmm) cc_final: 0.7762 (mmm) REVERT: C 472 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8195 (mtm110) REVERT: C 1148 ASP cc_start: 0.8163 (m-30) cc_final: 0.7851 (p0) outliers start: 14 outliers final: 6 residues processed: 78 average time/residue: 1.7029 time to fit residues: 141.3334 Evaluate side-chains 69 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.064303 restraints weight = 17339.340| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.35 r_work: 0.2756 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11119 Z= 0.112 Angle : 0.498 7.441 15252 Z= 0.271 Chirality : 0.037 0.156 1650 Planarity : 0.003 0.034 1801 Dihedral : 20.118 171.350 1903 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.16 % Allowed : 6.74 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1203 helix: 2.36 (0.22), residues: 578 sheet: -0.25 (0.65), residues: 67 loop : -0.64 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 PHE 0.011 0.001 PHE C 537 TYR 0.021 0.001 TYR C 86 ARG 0.005 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 519) hydrogen bonds : angle 3.90511 ( 1419) covalent geometry : bond 0.00238 (11119) covalent geometry : angle 0.49786 (15252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 394 LYS cc_start: 0.7869 (tppt) cc_final: 0.7387 (mmpt) REVERT: C 432 GLU cc_start: 0.7394 (pm20) cc_final: 0.6274 (pm20) REVERT: C 437 MET cc_start: 0.8247 (mmm) cc_final: 0.7891 (mmt) REVERT: C 472 ARG cc_start: 0.8434 (mtp85) cc_final: 0.8124 (mtm110) REVERT: C 1148 ASP cc_start: 0.8169 (m-30) cc_final: 0.7868 (p0) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 1.8126 time to fit residues: 136.8755 Evaluate side-chains 70 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 0.0470 chunk 71 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN C1131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.063353 restraints weight = 17097.594| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.35 r_work: 0.2734 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11119 Z= 0.125 Angle : 0.514 10.984 15252 Z= 0.278 Chirality : 0.038 0.161 1650 Planarity : 0.003 0.036 1801 Dihedral : 20.085 169.346 1903 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.16 % Allowed : 7.61 % Favored : 91.23 % 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: 1.36 (0.25), residues: 1203 helix: 2.37 (0.22), residues: 580 sheet: 0.02 (0.61), residues: 79 loop : -0.60 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 PHE 0.011 0.001 PHE C 537 TYR 0.022 0.001 TYR C 86 ARG 0.005 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 519) hydrogen bonds : angle 3.82663 ( 1419) covalent geometry : bond 0.00281 (11119) covalent geometry : angle 0.51408 (15252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 377 ARG cc_start: 0.8257 (tpp-160) cc_final: 0.7907 (tpp-160) REVERT: C 432 GLU cc_start: 0.7307 (pm20) cc_final: 0.6330 (pm20) REVERT: C 437 MET cc_start: 0.8277 (mmm) cc_final: 0.7937 (mmp) REVERT: C 469 ARG cc_start: 0.8479 (mtt180) cc_final: 0.8042 (mtt180) REVERT: C 1148 ASP cc_start: 0.8176 (m-30) cc_final: 0.7890 (p0) outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 1.8236 time to fit residues: 136.0691 Evaluate side-chains 69 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 0.0270 chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 100 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.096758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064593 restraints weight = 17169.632| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.33 r_work: 0.2766 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11119 Z= 0.109 Angle : 0.501 11.148 15252 Z= 0.269 Chirality : 0.037 0.156 1650 Planarity : 0.003 0.035 1801 Dihedral : 20.032 171.020 1903 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.25 % Allowed : 7.71 % Favored : 91.04 % 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: 1.40 (0.25), residues: 1203 helix: 2.47 (0.22), residues: 579 sheet: -0.18 (0.65), residues: 67 loop : -0.61 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 PHE 0.009 0.001 PHE C 782 TYR 0.021 0.001 TYR C 86 ARG 0.006 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 519) hydrogen bonds : angle 3.71688 ( 1419) covalent geometry : bond 0.00238 (11119) covalent geometry : angle 0.50100 (15252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: C 146 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9094 (tm) REVERT: C 377 ARG cc_start: 0.8314 (tpp-160) cc_final: 0.8048 (tpp-160) REVERT: C 394 LYS cc_start: 0.7921 (tppt) cc_final: 0.7423 (mmpt) REVERT: C 432 GLU cc_start: 0.7158 (pm20) cc_final: 0.6767 (pm20) REVERT: C 1127 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7808 (ttm-80) REVERT: C 1148 ASP cc_start: 0.8162 (m-30) cc_final: 0.7900 (p0) outliers start: 13 outliers final: 7 residues processed: 72 average time/residue: 1.8054 time to fit residues: 138.2554 Evaluate side-chains 69 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 chunk 101 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.096133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.063721 restraints weight = 17336.336| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.33 r_work: 0.2746 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11119 Z= 0.121 Angle : 0.516 12.285 15252 Z= 0.276 Chirality : 0.038 0.160 1650 Planarity : 0.003 0.036 1801 Dihedral : 20.022 168.966 1903 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.06 % Allowed : 8.57 % Favored : 90.37 % 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: 1.44 (0.25), residues: 1203 helix: 2.48 (0.22), residues: 579 sheet: 0.10 (0.61), residues: 79 loop : -0.61 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 PHE 0.011 0.001 PHE C 537 TYR 0.021 0.001 TYR C 86 ARG 0.004 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 519) hydrogen bonds : angle 3.70929 ( 1419) covalent geometry : bond 0.00271 (11119) covalent geometry : angle 0.51640 (15252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: C 146 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9103 (tm) REVERT: C 377 ARG cc_start: 0.8357 (tpp-160) cc_final: 0.8074 (tpp-160) REVERT: C 394 LYS cc_start: 0.7861 (tppt) cc_final: 0.7543 (mptt) REVERT: C 406 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: C 432 GLU cc_start: 0.7155 (pm20) cc_final: 0.6377 (pm20) REVERT: C 437 MET cc_start: 0.8004 (mmm) cc_final: 0.7502 (mmm) REVERT: C 472 ARG cc_start: 0.8333 (mtm110) cc_final: 0.8034 (ttp80) REVERT: C 1127 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7665 (ttm-80) REVERT: C 1148 ASP cc_start: 0.8170 (m-30) cc_final: 0.7908 (p0) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 1.6962 time to fit residues: 126.2894 Evaluate side-chains 71 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.093325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060442 restraints weight = 17471.571| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.37 r_work: 0.2674 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11119 Z= 0.207 Angle : 0.601 12.251 15252 Z= 0.322 Chirality : 0.042 0.174 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.178 171.527 1903 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.16 % Allowed : 8.57 % Favored : 90.27 % 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 (0.25), residues: 1203 helix: 2.27 (0.22), residues: 580 sheet: 0.01 (0.61), residues: 79 loop : -0.64 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 660 HIS 0.005 0.001 HIS C 976 PHE 0.015 0.002 PHE C 537 TYR 0.020 0.002 TYR C 86 ARG 0.003 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.06063 ( 519) hydrogen bonds : angle 3.95568 ( 1419) covalent geometry : bond 0.00496 (11119) covalent geometry : angle 0.60076 (15252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: C 146 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9110 (tm) REVERT: C 394 LYS cc_start: 0.7827 (tppt) cc_final: 0.7482 (mptt) REVERT: C 406 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: C 432 GLU cc_start: 0.7044 (pm20) cc_final: 0.6454 (pm20) REVERT: C 437 MET cc_start: 0.8094 (mmm) cc_final: 0.7753 (mmm) REVERT: C 638 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8665 (mmp) REVERT: C 1148 ASP cc_start: 0.8226 (m-30) cc_final: 0.7975 (p0) outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 1.6997 time to fit residues: 126.7186 Evaluate side-chains 73 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1109 MET Chi-restraints excluded: chain C residue 1147 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.094922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.062092 restraints weight = 17230.069| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.36 r_work: 0.2708 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11119 Z= 0.136 Angle : 0.545 12.935 15252 Z= 0.292 Chirality : 0.039 0.162 1650 Planarity : 0.003 0.037 1801 Dihedral : 20.138 169.634 1903 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.96 % Allowed : 8.96 % Favored : 90.08 % 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: 1.29 (0.25), residues: 1203 helix: 2.32 (0.22), residues: 580 sheet: 0.03 (0.61), residues: 79 loop : -0.66 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 PHE 0.010 0.001 PHE C 537 TYR 0.021 0.001 TYR C 86 ARG 0.007 0.000 ARG C 469 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 519) hydrogen bonds : angle 3.84207 ( 1419) covalent geometry : bond 0.00310 (11119) covalent geometry : angle 0.54536 (15252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: C 146 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9116 (tm) REVERT: C 377 ARG cc_start: 0.8278 (tpp-160) cc_final: 0.8018 (tpp-160) REVERT: C 394 LYS cc_start: 0.7881 (tppt) cc_final: 0.7355 (mmpt) REVERT: C 418 MET cc_start: 0.5011 (mtp) cc_final: 0.4636 (mmm) REVERT: C 432 GLU cc_start: 0.7107 (pm20) cc_final: 0.6388 (pm20) REVERT: C 437 MET cc_start: 0.8165 (mmm) cc_final: 0.7785 (mmm) REVERT: C 469 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8048 (ttt180) REVERT: C 638 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8637 (mmp) REVERT: C 1148 ASP cc_start: 0.8164 (m-30) cc_final: 0.7916 (p0) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 1.7983 time to fit residues: 133.8916 Evaluate side-chains 72 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 23 optimal weight: 0.0010 chunk 39 optimal weight: 0.3980 chunk 29 optimal weight: 0.2980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 610 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.096626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.064400 restraints weight = 17338.408| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.33 r_work: 0.2757 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11119 Z= 0.111 Angle : 0.515 12.623 15252 Z= 0.274 Chirality : 0.037 0.153 1650 Planarity : 0.003 0.036 1801 Dihedral : 20.056 171.820 1903 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.67 % Allowed : 9.15 % Favored : 90.17 % 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: 1.41 (0.25), residues: 1203 helix: 2.42 (0.22), residues: 580 sheet: 0.15 (0.62), residues: 79 loop : -0.62 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 696 HIS 0.004 0.001 HIS C1166 PHE 0.009 0.001 PHE C1021 TYR 0.022 0.001 TYR C 86 ARG 0.006 0.000 ARG C1127 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 519) hydrogen bonds : angle 3.67847 ( 1419) covalent geometry : bond 0.00240 (11119) covalent geometry : angle 0.51530 (15252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 146 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9112 (tm) REVERT: C 377 ARG cc_start: 0.8304 (tpp-160) cc_final: 0.8060 (tpp-160) REVERT: C 394 LYS cc_start: 0.7865 (tppt) cc_final: 0.7328 (mmpt) REVERT: C 417 ASP cc_start: 0.6272 (p0) cc_final: 0.5694 (p0) REVERT: C 432 GLU cc_start: 0.7027 (pm20) cc_final: 0.6330 (pm20) REVERT: C 437 MET cc_start: 0.8095 (mmm) cc_final: 0.7737 (mmm) REVERT: C 472 ARG cc_start: 0.8413 (mtm110) cc_final: 0.8161 (ttm110) REVERT: C 1148 ASP cc_start: 0.8141 (m-30) cc_final: 0.7890 (p0) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 1.7967 time to fit residues: 131.7107 Evaluate side-chains 70 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 0.0870 chunk 27 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 610 ASN C 794 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.066115 restraints weight = 17242.505| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.36 r_work: 0.2791 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11119 Z= 0.105 Angle : 0.513 13.819 15252 Z= 0.272 Chirality : 0.037 0.153 1650 Planarity : 0.002 0.035 1801 Dihedral : 19.964 172.680 1903 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.87 % Allowed : 9.34 % Favored : 89.79 % 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: 1.51 (0.25), residues: 1203 helix: 2.51 (0.22), residues: 579 sheet: 0.23 (0.63), residues: 79 loop : -0.56 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 696 HIS 0.003 0.001 HIS C1166 PHE 0.009 0.001 PHE C 886 TYR 0.022 0.001 TYR C 86 ARG 0.003 0.000 ARG C 472 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 519) hydrogen bonds : angle 3.58403 ( 1419) covalent geometry : bond 0.00226 (11119) covalent geometry : angle 0.51347 (15252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 146 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9158 (tm) REVERT: C 377 ARG cc_start: 0.8275 (tpp-160) cc_final: 0.8056 (tpp-160) REVERT: C 394 LYS cc_start: 0.7794 (tppt) cc_final: 0.7441 (mptt) REVERT: C 418 MET cc_start: 0.4555 (mmm) cc_final: 0.3965 (ptp) REVERT: C 432 GLU cc_start: 0.6941 (pm20) cc_final: 0.6184 (pm20) REVERT: C 437 MET cc_start: 0.8071 (mmm) cc_final: 0.7735 (mmm) REVERT: C 472 ARG cc_start: 0.8401 (mtm110) cc_final: 0.8177 (ttm110) REVERT: C 1148 ASP cc_start: 0.8148 (m-30) cc_final: 0.7873 (p0) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 1.7623 time to fit residues: 133.5496 Evaluate side-chains 70 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 421 GLN C 610 ASN C 794 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.096372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.063423 restraints weight = 17211.331| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.36 r_work: 0.2737 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11119 Z= 0.127 Angle : 0.538 12.627 15252 Z= 0.286 Chirality : 0.038 0.160 1650 Planarity : 0.003 0.037 1801 Dihedral : 19.995 168.803 1903 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.96 % Allowed : 9.63 % Favored : 89.40 % 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: 1.50 (0.25), residues: 1203 helix: 2.48 (0.22), residues: 579 sheet: 0.18 (0.63), residues: 79 loop : -0.55 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 401 HIS 0.002 0.001 HIS C 113 PHE 0.011 0.001 PHE C 537 TYR 0.021 0.001 TYR C 86 ARG 0.008 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 519) hydrogen bonds : angle 3.66270 ( 1419) covalent geometry : bond 0.00290 (11119) covalent geometry : angle 0.53783 (15252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10564.62 seconds wall clock time: 182 minutes 14.91 seconds (10934.91 seconds total)