Starting phenix.real_space_refine on Thu Aug 6 02:37:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klq_62413/08_2026/9klq_62413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klq_62413/08_2026/9klq_62413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9klq_62413/08_2026/9klq_62413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klq_62413/08_2026/9klq_62413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9klq_62413/08_2026/9klq_62413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klq_62413/08_2026/9klq_62413.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 147 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 7680 2.51 5 N 2397 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13055 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1284, 9958 Classifications: {'peptide': 1284} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 55, 'TRANS': 1228} Chain breaks: 10 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 6, 'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 129 Chain: "B" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2162 Classifications: {'RNA': 101} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 45, 'rna3p_pyr': 39} Link IDs: {'rna2p': 16, 'rna3p': 84} Chain breaks: 1 Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 386 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.22, per 1000 atoms: 0.17 Number of scatterers: 13055 At special positions: 0 Unit cell: (109.326, 118.916, 131.383, 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 33 16.00 P 147 15.00 Mg 2 11.99 O 2796 8.00 N 2397 7.00 C 7680 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: 0.90 Conformation dependent library (CDL) restraints added in 498.4 milliseconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 8 sheets defined 53.9% alpha, 8.6% beta 29 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 24 through 52 removed outlier: 3.603A pdb=" N ALA A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 54 No H-bonds generated for 'chain 'A' and resid 53 through 54' Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.560A pdb=" N LEU A 58 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 106 through 126 removed outlier: 3.573A pdb=" N GLY A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.928A pdb=" N LEU A 143 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.659A pdb=" N LEU A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.609A pdb=" N LYS A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.772A pdb=" N MET A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 269 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 278 through 284 removed outlier: 3.663A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.969A pdb=" N GLY A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 330 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.752A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 382 through 416 removed outlier: 3.560A pdb=" N PHE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 572 through 579 removed outlier: 3.748A pdb=" N LYS A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 691 through 704 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.614A pdb=" N LYS A 746 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.758A pdb=" N LYS A 752 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.599A pdb=" N VAL A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 895 Processing helix chain 'A' and resid 900 through 914 Processing helix chain 'A' and resid 936 through 966 removed outlier: 4.322A pdb=" N LYS A 953 " --> pdb=" O ARG A 949 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 996 through 1015 removed outlier: 3.517A pdb=" N LYS A1000 " --> pdb=" O GLU A 996 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A1001 " --> pdb=" O ALA A 997 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR A1002 " --> pdb=" O LYS A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1031 Processing helix chain 'A' and resid 1032 through 1035 Processing helix chain 'A' and resid 1054 through 1073 Proline residue: A1066 - end of helix Processing helix chain 'A' and resid 1075 through 1108 removed outlier: 3.736A pdb=" N LYS A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1115 removed outlier: 3.532A pdb=" N ALA A1114 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 4.026A pdb=" N ILE A1119 " --> pdb=" O THR A1116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A1120 " --> pdb=" O PRO A1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1116 through 1120' Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 3.539A pdb=" N LEU A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'A' and resid 1162 through 1190 removed outlier: 3.545A pdb=" N LEU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA A1168 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1243 removed outlier: 3.643A pdb=" N ALA A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1258 Processing helix chain 'A' and resid 1295 through 1309 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1328 through 1336 removed outlier: 4.216A pdb=" N GLY A1336 " --> pdb=" O GLU A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.905A pdb=" N LYS A1359 " --> pdb=" O PRO A1356 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY A1360 " --> pdb=" O ALA A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1376 removed outlier: 3.852A pdb=" N ASN A1366 " --> pdb=" O GLN A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1481 removed outlier: 3.619A pdb=" N ARG A1480 " --> pdb=" O GLN A1476 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A1481 " --> pdb=" O LEU A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1486 Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 562 removed outlier: 3.875A pdb=" N GLY A 669 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.552A pdb=" N LEU A 356 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 364 " --> pdb=" O LEU A 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 637 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 812 removed outlier: 3.595A pdb=" N ARG A 810 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 21.668A pdb=" N GLU A 824 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 17.072A pdb=" N PHE A 854 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 13.369A pdb=" N SER A 826 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N ARG A 852 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 828 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 852 " --> pdb=" O VAL A 778 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 774 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU A 764 " --> pdb=" O ILE A1218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 969 through 972 Processing sheet with id=AA7, first strand: chain 'A' and resid 1338 through 1341 Processing sheet with id=AA8, first strand: chain 'A' and resid 1387 through 1390 514 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2919 1.33 - 1.45: 3622 1.45 - 1.57: 6739 1.57 - 1.69: 289 1.69 - 1.81: 53 Bond restraints: 13622 Sorted by residual: bond pdb=" O3' A B 94 " pdb=" P U B 95 " ideal model delta sigma weight residual 1.607 1.535 0.072 1.20e-02 6.94e+03 3.64e+01 bond pdb=" C3' DT C 32 " pdb=" C2' DT C 32 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" P G B 93 " pdb=" O5' G B 93 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.00e-02 1.00e+04 8.11e+00 bond pdb=" C1' DT D 16 " pdb=" N1 DT D 16 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.55e+00 bond pdb=" O4' DT D 13 " pdb=" C1' DT D 13 " ideal model delta sigma weight residual 1.420 1.390 0.030 1.10e-02 8.26e+03 7.22e+00 ... (remaining 13617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 18430 2.10 - 4.21: 620 4.21 - 6.31: 42 6.31 - 8.41: 9 8.41 - 10.52: 4 Bond angle restraints: 19105 Sorted by residual: angle pdb=" O4' G B 92 " pdb=" C1' G B 92 " pdb=" N9 G B 92 " ideal model delta sigma weight residual 108.20 114.23 -6.03 8.00e-01 1.56e+00 5.69e+01 angle pdb=" C3' G B 92 " pdb=" O3' G B 92 " pdb=" P G B 93 " ideal model delta sigma weight residual 119.70 126.26 -6.56 1.20e+00 6.94e-01 2.99e+01 angle pdb=" C GLY A1281 " pdb=" N MET A1282 " pdb=" CA MET A1282 " ideal model delta sigma weight residual 121.90 115.30 6.60 1.26e+00 6.30e-01 2.75e+01 angle pdb=" C1' C B 26 " pdb=" N1 C B 26 " pdb=" C2 C B 26 " ideal model delta sigma weight residual 118.80 124.54 -5.74 1.10e+00 8.26e-01 2.72e+01 angle pdb=" C MET A1282 " pdb=" N ARG A1283 " pdb=" CA ARG A1283 " ideal model delta sigma weight residual 121.91 111.39 10.52 2.03e+00 2.43e-01 2.68e+01 ... (remaining 19100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.70: 7706 34.70 - 69.39: 440 69.39 - 104.09: 39 104.09 - 138.78: 2 138.78 - 173.48: 1 Dihedral angle restraints: 8188 sinusoidal: 4492 harmonic: 3696 Sorted by residual: dihedral pdb=" O4' C B 45 " pdb=" C1' C B 45 " pdb=" N1 C B 45 " pdb=" C2 C B 45 " ideal model delta sinusoidal sigma weight residual 200.00 26.52 173.48 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" CA ASP A1202 " pdb=" C ASP A1202 " pdb=" N PRO A1203 " pdb=" CA PRO A1203 " ideal model delta harmonic sigma weight residual 180.00 -151.53 -28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA GLN A1362 " pdb=" C GLN A1362 " pdb=" N ALA A1363 " pdb=" CA ALA A1363 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2029 0.102 - 0.205: 135 0.205 - 0.307: 2 0.307 - 0.410: 1 0.410 - 0.512: 6 Chirality restraints: 2173 Sorted by residual: chirality pdb=" P A B 103 " pdb=" OP1 A B 103 " pdb=" OP2 A B 103 " pdb=" O5' A B 103 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" P U B 67 " pdb=" OP1 U B 67 " pdb=" OP2 U B 67 " pdb=" O5' U B 67 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" P U B 95 " pdb=" OP1 U B 95 " pdb=" OP2 U B 95 " pdb=" O5' U B 95 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.05e+00 ... (remaining 2170 not shown) Planarity restraints: 1929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1202 " -0.086 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO A1203 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A1203 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO A1203 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 177 " 0.028 2.00e-02 2.50e+03 2.55e-02 1.63e+01 pdb=" CG TRP A 177 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 177 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 177 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 177 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 177 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 177 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 177 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 177 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 177 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " 0.020 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP A 135 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " 0.001 2.00e-02 2.50e+03 ... (remaining 1926 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 70 2.54 - 3.13: 9633 3.13 - 3.72: 20777 3.72 - 4.31: 27615 4.31 - 4.90: 44857 Nonbonded interactions: 102952 Sorted by model distance: nonbonded pdb=" OP2 U B 33 " pdb="MG MG B 201 " model vdw 1.956 2.170 nonbonded pdb=" OP2 U B 38 " pdb="MG MG B 202 " model vdw 2.091 2.170 nonbonded pdb=" OD2 ASP A1202 " pdb=" O2' G B 87 " model vdw 2.148 3.040 nonbonded pdb=" OD1 ASP A 957 " pdb=" NH1 ARG A 960 " model vdw 2.199 3.120 nonbonded pdb=" OG1 THR A 811 " pdb=" OE2 GLU A 824 " model vdw 2.207 3.040 ... (remaining 102947 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.006 0.072 13622 Z= 0.399 Angle : 0.778 10.515 19105 Z= 0.548 Chirality : 0.055 0.512 2173 Planarity : 0.006 0.130 1929 Dihedral : 19.045 173.476 5794 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.23 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1262 helix: 1.29 (0.21), residues: 643 sheet: -0.07 (0.47), residues: 124 loop : -1.40 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1484 TYR 0.012 0.001 TYR A 978 PHE 0.017 0.002 PHE A1348 TRP 0.068 0.002 TRP A 177 HIS 0.013 0.002 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.40 (13622) covalent geometry : angle 0.77802 / 0.55 (19105) hydrogen bonds : bond 0.14855 / 9.66 ( 587) hydrogen bonds : angle 5.71783 / 4.16 ( 1609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.354 Fit side-chains REVERT: A 175 ASP cc_start: 0.8219 (m-30) cc_final: 0.7758 (m-30) REVERT: A 972 MET cc_start: 0.8216 (mmp) cc_final: 0.7347 (mmm) REVERT: A 1006 MET cc_start: 0.7636 (ttp) cc_final: 0.7224 (ttp) REVERT: A 1061 ARG cc_start: 0.8530 (mtp180) cc_final: 0.7941 (mtp180) REVERT: A 1170 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8236 (mm-30) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1428 time to fit residues: 16.5847 Evaluate side-chains 65 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.114606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082798 restraints weight = 28248.340| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.65 r_work: 0.3110 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13622 Z= 0.143 Angle : 0.567 8.427 19105 Z= 0.324 Chirality : 0.038 0.205 2173 Planarity : 0.005 0.051 1929 Dihedral : 20.111 172.496 3463 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 0.91 % Allowed : 5.79 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1262 helix: 1.60 (0.21), residues: 647 sheet: 0.03 (0.46), residues: 124 loop : -1.22 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 670 TYR 0.012 0.001 TYR A 969 PHE 0.015 0.001 PHE A1348 TRP 0.027 0.001 TRP A 177 HIS 0.010 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (13622) covalent geometry : angle 0.56719 / 0.32 (19105) hydrogen bonds : bond 0.05538 / 3.83 ( 587) hydrogen bonds : angle 4.40670 / 3.21 ( 1609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.380 Fit side-chains REVERT: A 31 MET cc_start: 0.9120 (ttm) cc_final: 0.8896 (mtm) REVERT: A 175 ASP cc_start: 0.8257 (m-30) cc_final: 0.7909 (m-30) REVERT: A 177 TRP cc_start: 0.8493 (m100) cc_final: 0.8014 (m-10) REVERT: A 969 TYR cc_start: 0.7976 (p90) cc_final: 0.7659 (p90) REVERT: A 972 MET cc_start: 0.8285 (mmp) cc_final: 0.7455 (mmm) REVERT: A 1006 MET cc_start: 0.7855 (ttp) cc_final: 0.7385 (ttp) REVERT: A 1061 ARG cc_start: 0.8540 (mtp180) cc_final: 0.8061 (mtp180) REVERT: A 1282 MET cc_start: 0.6001 (pmm) cc_final: 0.5429 (pmm) REVERT: A 1304 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6583 (pm20) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.1371 time to fit residues: 14.0901 Evaluate side-chains 73 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 136 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 116 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A1221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081504 restraints weight = 28734.831| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.67 r_work: 0.3076 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13622 Z= 0.182 Angle : 0.556 8.154 19105 Z= 0.315 Chirality : 0.038 0.184 2173 Planarity : 0.004 0.047 1929 Dihedral : 20.107 171.794 3463 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 0.81 % Allowed : 9.04 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.24), residues: 1262 helix: 1.65 (0.20), residues: 649 sheet: -0.06 (0.45), residues: 124 loop : -1.29 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1484 TYR 0.010 0.001 TYR A 978 PHE 0.014 0.001 PHE A1348 TRP 0.028 0.002 TRP A 177 HIS 0.010 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (13622) covalent geometry : angle 0.55575 / 0.32 (19105) hydrogen bonds : bond 0.05571 / 3.84 ( 587) hydrogen bonds : angle 4.23106 / 3.08 ( 1609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8299 (m-30) cc_final: 0.7965 (m-30) REVERT: A 969 TYR cc_start: 0.7968 (p90) cc_final: 0.7676 (p90) REVERT: A 972 MET cc_start: 0.8218 (mmp) cc_final: 0.7801 (mmm) REVERT: A 1006 MET cc_start: 0.7771 (ttp) cc_final: 0.7269 (ttp) REVERT: A 1061 ARG cc_start: 0.8533 (mtp180) cc_final: 0.8052 (mtp180) REVERT: A 1483 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7178 (tt) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.1267 time to fit residues: 12.7940 Evaluate side-chains 69 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 134 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 119 optimal weight: 0.0980 chunk 137 optimal weight: 40.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A1221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083367 restraints weight = 28476.190| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.67 r_work: 0.3119 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13622 Z= 0.123 Angle : 0.499 8.579 19105 Z= 0.289 Chirality : 0.036 0.175 2173 Planarity : 0.004 0.046 1929 Dihedral : 20.085 171.793 3463 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 1.42 % Allowed : 10.66 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1262 helix: 1.92 (0.21), residues: 643 sheet: 0.04 (0.46), residues: 119 loop : -1.16 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1313 TYR 0.009 0.001 TYR A 978 PHE 0.011 0.001 PHE A 772 TRP 0.018 0.001 TRP A 177 HIS 0.007 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (13622) covalent geometry : angle 0.49933 / 0.29 (19105) hydrogen bonds : bond 0.04726 / 3.29 ( 587) hydrogen bonds : angle 4.01575 / 2.93 ( 1609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8286 (m-30) cc_final: 0.7949 (m-30) REVERT: A 969 TYR cc_start: 0.7945 (p90) cc_final: 0.7648 (p90) REVERT: A 972 MET cc_start: 0.8219 (mmp) cc_final: 0.7796 (mmm) REVERT: A 1006 MET cc_start: 0.7751 (ttp) cc_final: 0.7250 (ttp) REVERT: A 1027 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6576 (tp) REVERT: A 1061 ARG cc_start: 0.8457 (mtp180) cc_final: 0.7957 (mtp180) REVERT: A 1069 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 1285 GLN cc_start: 0.8408 (tt0) cc_final: 0.8163 (tt0) REVERT: A 1483 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7099 (tt) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 0.1103 time to fit residues: 12.6221 Evaluate side-chains 79 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1221 ASN Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 2 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081536 restraints weight = 28795.281| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.69 r_work: 0.3078 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13622 Z= 0.196 Angle : 0.553 8.596 19105 Z= 0.311 Chirality : 0.038 0.180 2173 Planarity : 0.005 0.052 1929 Dihedral : 20.107 171.459 3463 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 1.83 % Allowed : 12.28 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1262 helix: 1.82 (0.21), residues: 645 sheet: -0.11 (0.45), residues: 124 loop : -1.25 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 849 TYR 0.010 0.001 TYR A 978 PHE 0.013 0.001 PHE A 712 TRP 0.020 0.002 TRP A 177 HIS 0.008 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (13622) covalent geometry : angle 0.55312 / 0.31 (19105) hydrogen bonds : bond 0.05283 / 3.65 ( 587) hydrogen bonds : angle 4.11224 / 3.00 ( 1609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.286 Fit side-chains REVERT: A 175 ASP cc_start: 0.8302 (m-30) cc_final: 0.7982 (m-30) REVERT: A 344 LEU cc_start: 0.9065 (tp) cc_final: 0.8856 (tp) REVERT: A 969 TYR cc_start: 0.7928 (p90) cc_final: 0.7647 (p90) REVERT: A 972 MET cc_start: 0.8239 (mmp) cc_final: 0.7525 (mmm) REVERT: A 1006 MET cc_start: 0.7773 (ttp) cc_final: 0.7341 (ttp) REVERT: A 1027 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6711 (tp) REVERT: A 1061 ARG cc_start: 0.8305 (mtp180) cc_final: 0.7902 (mtp180) REVERT: A 1069 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 1239 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7046 (tt) REVERT: A 1285 GLN cc_start: 0.8498 (tt0) cc_final: 0.8197 (tt0) REVERT: A 1304 GLN cc_start: 0.6792 (pm20) cc_final: 0.6583 (pm20) REVERT: A 1439 MET cc_start: 0.6616 (ptp) cc_final: 0.6060 (ptt) outliers start: 18 outliers final: 6 residues processed: 81 average time/residue: 0.1107 time to fit residues: 12.9698 Evaluate side-chains 71 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 1 optimal weight: 0.0070 chunk 139 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 overall best weight: 1.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.113989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.082235 restraints weight = 28417.756| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.67 r_work: 0.3092 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13622 Z= 0.156 Angle : 0.521 9.162 19105 Z= 0.295 Chirality : 0.037 0.178 2173 Planarity : 0.004 0.049 1929 Dihedral : 20.103 171.297 3463 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 1.62 % Allowed : 12.99 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1262 helix: 1.90 (0.21), residues: 645 sheet: -0.01 (0.46), residues: 119 loop : -1.23 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1313 TYR 0.009 0.001 TYR A 978 PHE 0.011 0.001 PHE A 712 TRP 0.019 0.001 TRP A 177 HIS 0.007 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (13622) covalent geometry : angle 0.52099 / 0.29 (19105) hydrogen bonds : bond 0.04978 / 3.46 ( 587) hydrogen bonds : angle 4.02406 / 2.94 ( 1609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8279 (m-30) cc_final: 0.7965 (m-30) REVERT: A 969 TYR cc_start: 0.7918 (p90) cc_final: 0.7644 (p90) REVERT: A 972 MET cc_start: 0.8256 (mmp) cc_final: 0.7578 (mmm) REVERT: A 1006 MET cc_start: 0.7847 (ttp) cc_final: 0.7425 (ttp) REVERT: A 1027 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6656 (tp) REVERT: A 1061 ARG cc_start: 0.8297 (mtp180) cc_final: 0.7852 (mtp180) REVERT: A 1069 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 1239 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7037 (tt) REVERT: A 1439 MET cc_start: 0.6567 (ptp) cc_final: 0.6019 (ptt) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.1067 time to fit residues: 12.0480 Evaluate side-chains 75 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1373 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082445 restraints weight = 28383.236| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.67 r_work: 0.3093 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13622 Z= 0.148 Angle : 0.519 10.428 19105 Z= 0.291 Chirality : 0.036 0.178 2173 Planarity : 0.004 0.054 1929 Dihedral : 20.079 171.596 3463 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 1.42 % Allowed : 13.50 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1262 helix: 1.98 (0.21), residues: 645 sheet: 0.06 (0.47), residues: 119 loop : -1.21 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1313 TYR 0.009 0.001 TYR A 978 PHE 0.011 0.001 PHE A 712 TRP 0.019 0.001 TRP A 177 HIS 0.007 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (13622) covalent geometry : angle 0.51898 / 0.29 (19105) hydrogen bonds : bond 0.04836 / 3.37 ( 587) hydrogen bonds : angle 3.97299 / 2.91 ( 1609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8276 (m-30) cc_final: 0.7959 (m-30) REVERT: A 866 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: A 969 TYR cc_start: 0.7873 (p90) cc_final: 0.7618 (p90) REVERT: A 972 MET cc_start: 0.8249 (mmp) cc_final: 0.7606 (mmm) REVERT: A 1006 MET cc_start: 0.7889 (ttp) cc_final: 0.7457 (ttp) REVERT: A 1027 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6637 (tp) REVERT: A 1061 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7884 (mtp180) REVERT: A 1069 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: A 1239 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6813 (tt) outliers start: 14 outliers final: 10 residues processed: 80 average time/residue: 0.1152 time to fit residues: 13.0228 Evaluate side-chains 79 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1373 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.111923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080022 restraints weight = 28404.823| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.66 r_work: 0.3049 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13622 Z= 0.249 Angle : 0.603 11.248 19105 Z= 0.331 Chirality : 0.041 0.194 2173 Planarity : 0.005 0.054 1929 Dihedral : 20.154 170.461 3463 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 2.03 % Allowed : 13.50 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1262 helix: 1.68 (0.20), residues: 645 sheet: -0.18 (0.45), residues: 124 loop : -1.36 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1313 TYR 0.012 0.001 TYR A1250 PHE 0.017 0.002 PHE A 712 TRP 0.024 0.002 TRP A 177 HIS 0.009 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.25 (13622) covalent geometry : angle 0.60252 / 0.33 (19105) hydrogen bonds : bond 0.05874 / 4.05 ( 587) hydrogen bonds : angle 4.23202 / 3.10 ( 1609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8299 (m-30) cc_final: 0.7898 (m-30) REVERT: A 969 TYR cc_start: 0.7894 (p90) cc_final: 0.7643 (p90) REVERT: A 972 MET cc_start: 0.8250 (mmp) cc_final: 0.7764 (mmm) REVERT: A 1006 MET cc_start: 0.7906 (ttp) cc_final: 0.7477 (ttp) REVERT: A 1061 ARG cc_start: 0.8305 (mtp180) cc_final: 0.7883 (mtp180) REVERT: A 1069 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: A 1239 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6744 (tt) outliers start: 20 outliers final: 12 residues processed: 82 average time/residue: 0.1090 time to fit residues: 12.5401 Evaluate side-chains 78 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 61 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 86 optimal weight: 0.0170 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 614 GLN A1481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.115316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.083684 restraints weight = 28590.877| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.68 r_work: 0.3120 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13622 Z= 0.113 Angle : 0.513 9.658 19105 Z= 0.287 Chirality : 0.035 0.180 2173 Planarity : 0.004 0.053 1929 Dihedral : 20.064 171.573 3463 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 1.12 % Allowed : 14.62 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1262 helix: 2.06 (0.21), residues: 640 sheet: 0.01 (0.47), residues: 119 loop : -1.11 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1313 TYR 0.007 0.001 TYR A 978 PHE 0.008 0.001 PHE A 772 TRP 0.015 0.001 TRP A 177 HIS 0.007 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (13622) covalent geometry : angle 0.51287 / 0.29 (19105) hydrogen bonds : bond 0.04431 / 3.11 ( 587) hydrogen bonds : angle 3.91247 / 2.85 ( 1609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8250 (m-30) cc_final: 0.7930 (m-30) REVERT: A 969 TYR cc_start: 0.7829 (p90) cc_final: 0.7574 (p90) REVERT: A 972 MET cc_start: 0.8205 (mmp) cc_final: 0.7559 (mmm) REVERT: A 1006 MET cc_start: 0.7867 (ttp) cc_final: 0.7462 (ttp) REVERT: A 1061 ARG cc_start: 0.8295 (mtp180) cc_final: 0.7893 (mtp180) REVERT: A 1069 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: A 1239 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6534 (tt) REVERT: A 1282 MET cc_start: 0.6461 (pmm) cc_final: 0.5971 (pmm) outliers start: 11 outliers final: 7 residues processed: 82 average time/residue: 0.1356 time to fit residues: 15.0152 Evaluate side-chains 78 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 672 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.114689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082806 restraints weight = 28751.226| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.69 r_work: 0.3103 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13622 Z= 0.133 Angle : 0.510 8.710 19105 Z= 0.286 Chirality : 0.036 0.177 2173 Planarity : 0.004 0.053 1929 Dihedral : 20.029 172.180 3463 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 1.02 % Allowed : 14.62 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1262 helix: 2.03 (0.21), residues: 645 sheet: 0.02 (0.47), residues: 119 loop : -1.12 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1484 TYR 0.008 0.001 TYR A 978 PHE 0.010 0.001 PHE A 712 TRP 0.017 0.001 TRP A 177 HIS 0.007 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (13622) covalent geometry : angle 0.50961 / 0.29 (19105) hydrogen bonds : bond 0.04625 / 3.22 ( 587) hydrogen bonds : angle 3.90946 / 2.85 ( 1609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8256 (m-30) cc_final: 0.7927 (m-30) REVERT: A 969 TYR cc_start: 0.7830 (p90) cc_final: 0.7571 (p90) REVERT: A 1006 MET cc_start: 0.7852 (ttp) cc_final: 0.7455 (ttp) REVERT: A 1061 ARG cc_start: 0.8301 (mtp180) cc_final: 0.7894 (mtp180) REVERT: A 1069 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 1239 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6515 (tt) REVERT: A 1282 MET cc_start: 0.6401 (pmm) cc_final: 0.6175 (pmm) REVERT: A 1285 GLN cc_start: 0.8415 (tt0) cc_final: 0.8126 (tt0) REVERT: A 1466 GLU cc_start: 0.8347 (tp30) cc_final: 0.8138 (tp30) outliers start: 10 outliers final: 7 residues processed: 75 average time/residue: 0.1227 time to fit residues: 12.8069 Evaluate side-chains 75 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 672 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.114484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082718 restraints weight = 28563.356| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.68 r_work: 0.3102 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13622 Z= 0.139 Angle : 0.516 10.032 19105 Z= 0.286 Chirality : 0.036 0.185 2173 Planarity : 0.004 0.055 1929 Dihedral : 20.040 172.180 3463 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 1.12 % Allowed : 14.62 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1262 helix: 2.02 (0.21), residues: 645 sheet: 0.05 (0.47), residues: 119 loop : -1.15 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1392 TYR 0.008 0.001 TYR A 978 PHE 0.010 0.001 PHE A 712 TRP 0.017 0.001 TRP A 177 HIS 0.007 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (13622) covalent geometry : angle 0.51612 / 0.29 (19105) hydrogen bonds : bond 0.04656 / 3.25 ( 587) hydrogen bonds : angle 3.90254 / 2.84 ( 1609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2364.20 seconds wall clock time: 41 minutes 9.46 seconds (2469.46 seconds total)