Starting phenix.real_space_refine on Thu Sep 18 01:48:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klq_62413/09_2025/9klq_62413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klq_62413/09_2025/9klq_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_62413/09_2025/9klq_62413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klq_62413/09_2025/9klq_62413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9klq_62413/09_2025/9klq_62413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klq_62413/09_2025/9klq_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-2.0-5805/lib/python3.9/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: 3.12, per 1000 atoms: 0.24 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: 1.28 Conformation dependent library (CDL) restraints added in 523.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.77 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: 3.17 Time building geometry restraints manager: 1.68 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 1.50e-02 4.44e+03 2.33e+01 bond pdb=" O5' G B 93 " pdb=" C5' G B 93 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.46e+00 bond pdb=" O5' U B 67 " pdb=" C5' U B 67 " ideal model delta sigma weight residual 1.420 1.450 -0.030 1.50e-02 4.44e+03 3.94e+00 bond pdb=" P G B 93 " pdb=" O5' G B 93 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.50e-02 4.44e+03 3.61e+00 bond pdb=" O5' U B 95 " pdb=" C5' U B 95 " ideal model delta sigma weight residual 1.420 1.448 -0.028 1.50e-02 4.44e+03 3.60e+00 ... (remaining 13617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 18691 2.10 - 4.21: 359 4.21 - 6.31: 43 6.31 - 8.41: 8 8.41 - 10.52: 4 Bond angle restraints: 19105 Sorted by residual: 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=" 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 angle pdb=" C LYS A 231 " pdb=" CA LYS A 231 " pdb=" CB LYS A 231 " ideal model delta sigma weight residual 117.23 110.31 6.92 1.36e+00 5.41e-01 2.59e+01 angle pdb=" C3' G B 92 " pdb=" O3' G B 92 " pdb=" P G B 93 " ideal model delta sigma weight residual 120.20 126.26 -6.06 1.50e+00 4.44e-01 1.63e+01 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 1.50e+00 4.44e-01 1.62e+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: 2120 0.102 - 0.205: 44 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: 2.800 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.130 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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= 0.266 Angle : 0.695 10.515 19105 Z= 0.373 Chirality : 0.047 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 aren 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 covalent geometry : bond 0.00575 (13622) covalent geometry : angle 0.69548 (19105) hydrogen bonds : bond 0.14855 ( 587) hydrogen bonds : angle 5.71783 ( 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 : 0.428 Fit side-chains REVERT: A 175 ASP cc_start: 0.8219 (m-30) cc_final: 0.7758 (m-30) REVERT: A 960 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7769 (mtt180) 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: 0.7225 (ttp) REVERT: A 1061 ARG cc_start: 0.8530 (mtp180) cc_final: 0.7942 (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: 0.1712 time to fit residues: 19.5204 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 : 0.456 ------------------------------------------------------------------------------- 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: 8.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.115083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083341 restraints weight = 28281.237| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.66 r_work: 0.3117 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0993 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= 0.137 Angle : 0.549 8.500 19105 Z= 0.296 Chirality : 0.036 0.307 2173 Planarity : 0.004 0.052 1929 Dihedral : 20.052 175.405 3463 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 0.71 % Allowed : 5.99 % 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 aren not related in a simple way. whole: 0.64 (0.24), residues: 1262 helix: 1.71 (0.21), residues: 646 sheet: 0.01 (0.47), residues: 119 loop : -1.22 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1484 TYR 0.013 0.001 TYR A 969 PHE 0.013 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 covalent geometry : bond 0.00293 (13622) covalent geometry : angle 0.54875 (19105) hydrogen bonds : bond 0.04821 ( 587) hydrogen bonds : angle 4.19674 ( 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 81 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8264 (m-30) cc_final: 0.7917 (m-30) REVERT: A 177 TRP cc_start: 0.8469 (m100) cc_final: 0.7938 (m-10) REVERT: A 969 TYR cc_start: 0.8000 (p90) cc_final: 0.7701 (p90) REVERT: A 972 MET cc_start: 0.8312 (mmp) cc_final: 0.7791 (mmm) REVERT: A 1006 MET cc_start: 0.7844 (ttp) cc_final: 0.7359 (ttp) REVERT: A 1061 ARG cc_start: 0.8574 (mtp180) cc_final: 0.8068 (mtp180) REVERT: A 1282 MET cc_start: 0.6093 (pmm) cc_final: 0.5485 (pmm) REVERT: A 1285 GLN cc_start: 0.8370 (tt0) cc_final: 0.8111 (tt0) REVERT: A 1304 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6635 (pm20) REVERT: A 1483 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7163 (tt) outliers start: 7 outliers final: 4 residues processed: 79 average time/residue: 0.1568 time to fit residues: 16.5421 Evaluate side-chains 73 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 1304 GLN Chi-restraints excluded: chain A residue 1361 LEU 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: 8.9990 chunk 111 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3762 r_free = 0.3762 target = 0.112486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080479 restraints weight = 28780.259| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.68 r_work: 0.3059 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13622 Z= 0.227 Angle : 0.590 8.357 19105 Z= 0.317 Chirality : 0.038 0.338 2173 Planarity : 0.005 0.047 1929 Dihedral : 20.115 173.868 3463 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 1.02 % Allowed : 9.75 % Favored : 89.24 % 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 aren not related in a simple way. whole: 0.44 (0.24), residues: 1262 helix: 1.59 (0.20), residues: 649 sheet: -0.42 (0.45), residues: 134 loop : -1.32 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 541 TYR 0.012 0.001 TYR A 978 PHE 0.014 0.002 PHE A1348 TRP 0.032 0.002 TRP A 177 HIS 0.011 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00509 (13622) covalent geometry : angle 0.59028 (19105) hydrogen bonds : bond 0.05694 ( 587) hydrogen bonds : angle 4.24552 ( 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 82 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.358 Fit side-chains REVERT: A 125 ARG cc_start: 0.7542 (mmt-90) cc_final: 0.7128 (mmt-90) REVERT: A 175 ASP cc_start: 0.8332 (m-30) cc_final: 0.8016 (m-30) REVERT: A 969 TYR cc_start: 0.7932 (p90) cc_final: 0.7629 (p90) REVERT: A 972 MET cc_start: 0.8239 (mmp) cc_final: 0.7819 (mmm) REVERT: A 1006 MET cc_start: 0.7787 (ttp) cc_final: 0.7321 (ttp) REVERT: A 1061 ARG cc_start: 0.8332 (mtp180) cc_final: 0.7827 (mtp180) REVERT: A 1170 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8284 (mm-30) REVERT: A 1291 THR cc_start: 0.7749 (m) cc_final: 0.7542 (p) REVERT: A 1304 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6744 (pm20) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 0.1611 time to fit residues: 16.7759 Evaluate side-chains 74 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 966 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 614 GLN A1221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.114917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083148 restraints weight = 28512.794| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.67 r_work: 0.3108 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13622 Z= 0.131 Angle : 0.509 8.477 19105 Z= 0.274 Chirality : 0.034 0.295 2173 Planarity : 0.004 0.045 1929 Dihedral : 20.035 176.420 3463 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 1.02 % Allowed : 11.47 % Favored : 87.51 % 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 aren not related in a simple way. whole: 0.89 (0.24), residues: 1262 helix: 1.97 (0.21), residues: 643 sheet: 0.09 (0.47), residues: 119 loop : -1.16 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1313 TYR 0.009 0.001 TYR A 978 PHE 0.010 0.001 PHE A 712 TRP 0.018 0.001 TRP A 177 HIS 0.008 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00285 (13622) covalent geometry : angle 0.50871 (19105) hydrogen bonds : bond 0.04395 ( 587) hydrogen bonds : angle 3.87934 ( 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: 10 poor density : 75 time to evaluate : 0.327 Fit side-chains REVERT: A 175 ASP cc_start: 0.8279 (m-30) cc_final: 0.7952 (m-30) REVERT: A 972 MET cc_start: 0.8252 (mmp) cc_final: 0.7918 (mmm) REVERT: A 1006 MET cc_start: 0.7692 (ttp) cc_final: 0.7208 (ttp) REVERT: A 1027 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6556 (tp) REVERT: A 1061 ARG cc_start: 0.8414 (mtp180) cc_final: 0.7988 (mtp180) REVERT: A 1069 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 1285 GLN cc_start: 0.8345 (tt0) cc_final: 0.8087 (tt0) REVERT: A 1291 THR cc_start: 0.7667 (m) cc_final: 0.7439 (p) REVERT: A 1304 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6731 (pm20) outliers start: 10 outliers final: 4 residues processed: 84 average time/residue: 0.1564 time to fit residues: 17.7397 Evaluate side-chains 75 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 1027 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1221 ASN Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1361 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: 6.9990 chunk 118 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3796 r_free = 0.3796 target = 0.114841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083105 restraints weight = 28616.720| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.68 r_work: 0.3107 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13622 Z= 0.133 Angle : 0.513 8.547 19105 Z= 0.274 Chirality : 0.034 0.298 2173 Planarity : 0.004 0.050 1929 Dihedral : 20.040 176.982 3463 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 1.62 % Allowed : 11.88 % Favored : 86.50 % 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 aren not related in a simple way. whole: 0.93 (0.24), residues: 1262 helix: 2.01 (0.21), residues: 645 sheet: 0.13 (0.47), residues: 119 loop : -1.18 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 960 TYR 0.015 0.001 TYR A 969 PHE 0.009 0.001 PHE A 712 TRP 0.015 0.001 TRP A 177 HIS 0.008 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00289 (13622) covalent geometry : angle 0.51299 (19105) hydrogen bonds : bond 0.04395 ( 587) hydrogen bonds : angle 3.84387 ( 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 87 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.264 Fit side-chains REVERT: A 175 ASP cc_start: 0.8275 (m-30) cc_final: 0.7955 (m-30) REVERT: A 972 MET cc_start: 0.8255 (mmp) cc_final: 0.7917 (mmm) REVERT: A 1006 MET cc_start: 0.7694 (ttp) cc_final: 0.7259 (ttp) REVERT: A 1027 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6524 (tp) REVERT: A 1061 ARG cc_start: 0.8329 (mtp180) cc_final: 0.7899 (mtp180) REVERT: A 1069 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: A 1239 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6855 (tt) REVERT: A 1285 GLN cc_start: 0.8309 (tt0) cc_final: 0.8067 (tt0) REVERT: A 1304 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6713 (pm20) outliers start: 16 outliers final: 7 residues processed: 85 average time/residue: 0.1452 time to fit residues: 16.9657 Evaluate side-chains 78 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 709 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1304 GLN 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: 0.6980 chunk 139 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3772 r_free = 0.3772 target = 0.113174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.081330 restraints weight = 28352.504| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.66 r_work: 0.3072 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13622 Z= 0.193 Angle : 0.549 8.570 19105 Z= 0.294 Chirality : 0.036 0.326 2173 Planarity : 0.004 0.054 1929 Dihedral : 20.112 175.501 3463 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 1.73 % Allowed : 12.79 % Favored : 85.48 % 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 aren not related in a simple way. whole: 0.76 (0.24), residues: 1262 helix: 1.87 (0.21), residues: 645 sheet: 0.01 (0.46), residues: 124 loop : -1.25 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 960 TYR 0.017 0.001 TYR A 969 PHE 0.018 0.001 PHE A 772 TRP 0.020 0.001 TRP A 177 HIS 0.008 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00432 (13622) covalent geometry : angle 0.54950 (19105) hydrogen bonds : bond 0.05121 ( 587) hydrogen bonds : angle 3.98915 ( 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: 17 poor density : 65 time to evaluate : 0.395 Fit side-chains REVERT: A 175 ASP cc_start: 0.8282 (m-30) cc_final: 0.7973 (m-30) REVERT: A 972 MET cc_start: 0.8293 (mmp) cc_final: 0.7692 (mmm) REVERT: A 1006 MET cc_start: 0.7852 (ttp) cc_final: 0.7467 (ttp) REVERT: A 1027 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6669 (tp) REVERT: A 1061 ARG cc_start: 0.8316 (mtp180) cc_final: 0.7898 (mtp180) REVERT: A 1069 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 1239 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6633 (tt) REVERT: A 1282 MET cc_start: 0.6421 (pmm) cc_final: 0.6083 (pmm) outliers start: 17 outliers final: 7 residues processed: 80 average time/residue: 0.1476 time to fit residues: 16.0853 Evaluate side-chains 74 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 709 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1221 ASN Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 18 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 15 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 672 GLN A1221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.114271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082483 restraints weight = 28401.634| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.68 r_work: 0.3097 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1682 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= 0.145 Angle : 0.529 8.634 19105 Z= 0.282 Chirality : 0.035 0.308 2173 Planarity : 0.004 0.056 1929 Dihedral : 20.087 176.207 3463 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.68 % Favored : 95.25 % Rotamer: Outliers : 1.52 % Allowed : 13.40 % 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 aren not related in a simple way. whole: 0.90 (0.24), residues: 1262 helix: 1.97 (0.21), residues: 645 sheet: 0.13 (0.47), residues: 119 loop : -1.17 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1392 TYR 0.016 0.001 TYR A 969 PHE 0.009 0.001 PHE A 712 TRP 0.016 0.001 TRP A 177 HIS 0.007 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00319 (13622) covalent geometry : angle 0.52880 (19105) hydrogen bonds : bond 0.04592 ( 587) hydrogen bonds : angle 3.89595 ( 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 84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.389 Fit side-chains REVERT: A 175 ASP cc_start: 0.8271 (m-30) cc_final: 0.7960 (m-30) REVERT: A 972 MET cc_start: 0.8289 (mmp) cc_final: 0.7787 (mmm) REVERT: A 1006 MET cc_start: 0.7860 (ttp) cc_final: 0.7465 (ttp) REVERT: A 1027 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6589 (tp) REVERT: A 1061 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7886 (mtp180) REVERT: A 1069 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 1239 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6529 (tt) REVERT: A 1282 MET cc_start: 0.6274 (pmm) cc_final: 0.5603 (pmm) REVERT: A 1283 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.6006 (mtt180) REVERT: A 1285 GLN cc_start: 0.8331 (tt0) cc_final: 0.8061 (tt0) outliers start: 15 outliers final: 10 residues processed: 83 average time/residue: 0.1418 time to fit residues: 16.3698 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 : 0.375 ------------------------------------------------------------------------------- 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 283 LEU 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 1027 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1221 ASN Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1283 ARG Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1361 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: 10.0000 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 0.0470 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 614 GLN A 672 GLN A1221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.111918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079944 restraints weight = 28425.933| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.66 r_work: 0.3051 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13622 Z= 0.242 Angle : 0.605 10.613 19105 Z= 0.323 Chirality : 0.038 0.344 2173 Planarity : 0.005 0.060 1929 Dihedral : 20.173 174.306 3463 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.47 % Favored : 94.45 % Rotamer: Outliers : 1.62 % Allowed : 13.50 % Favored : 84.87 % 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 aren not related in a simple way. whole: 0.59 (0.24), residues: 1262 helix: 1.71 (0.21), residues: 643 sheet: -0.03 (0.46), residues: 124 loop : -1.30 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1283 TYR 0.019 0.001 TYR A 969 PHE 0.015 0.001 PHE A 712 TRP 0.021 0.002 TRP A 177 HIS 0.008 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00544 (13622) covalent geometry : angle 0.60548 (19105) hydrogen bonds : bond 0.05633 ( 587) hydrogen bonds : angle 4.19210 ( 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 78 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.414 Fit side-chains REVERT: A 125 ARG cc_start: 0.7752 (mmt-90) cc_final: 0.7198 (mtt-85) REVERT: A 175 ASP cc_start: 0.8313 (m-30) cc_final: 0.8016 (m-30) REVERT: A 972 MET cc_start: 0.8266 (mmp) cc_final: 0.7689 (mmm) REVERT: A 1006 MET cc_start: 0.7901 (ttp) cc_final: 0.7478 (ttp) REVERT: A 1061 ARG cc_start: 0.8303 (mtp180) cc_final: 0.7887 (mtp180) REVERT: A 1069 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 1239 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6615 (tt) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.1371 time to fit residues: 15.0628 Evaluate side-chains 74 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 283 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1405 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 614 GLN A 672 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.114656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082980 restraints weight = 28668.877| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.68 r_work: 0.3107 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13622 Z= 0.135 Angle : 0.527 9.085 19105 Z= 0.281 Chirality : 0.035 0.299 2173 Planarity : 0.004 0.058 1929 Dihedral : 20.060 176.463 3463 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 1.52 % Allowed : 14.31 % Favored : 84.16 % 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 aren not related in a simple way. whole: 0.94 (0.24), residues: 1262 helix: 2.00 (0.21), residues: 642 sheet: 0.11 (0.47), residues: 119 loop : -1.12 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 960 TYR 0.016 0.001 TYR A 969 PHE 0.009 0.001 PHE A 712 TRP 0.014 0.001 TRP A 177 HIS 0.007 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00294 (13622) covalent geometry : angle 0.52690 (19105) hydrogen bonds : bond 0.04412 ( 587) hydrogen bonds : angle 3.90705 ( 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 84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.480 Fit side-chains REVERT: A 175 ASP cc_start: 0.8269 (m-30) cc_final: 0.7953 (m-30) REVERT: A 972 MET cc_start: 0.8294 (mmp) cc_final: 0.7805 (mmm) REVERT: A 1006 MET cc_start: 0.7889 (ttp) cc_final: 0.7508 (ttp) REVERT: A 1061 ARG cc_start: 0.8269 (mtp180) cc_final: 0.7871 (mtp180) REVERT: A 1069 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 1239 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6401 (tt) REVERT: A 1282 MET cc_start: 0.6389 (pmm) cc_final: 0.6007 (pmm) REVERT: A 1285 GLN cc_start: 0.8342 (tt0) cc_final: 0.8071 (tt0) outliers start: 15 outliers final: 8 residues processed: 83 average time/residue: 0.1549 time to fit residues: 17.4709 Evaluate side-chains 76 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1239 LEU 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: 0.3980 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 57 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3793 r_free = 0.3793 target = 0.114665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082965 restraints weight = 28627.404| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.67 r_work: 0.3105 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13622 Z= 0.137 Angle : 0.534 8.945 19105 Z= 0.283 Chirality : 0.035 0.303 2173 Planarity : 0.004 0.057 1929 Dihedral : 20.051 177.242 3463 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 1.42 % Allowed : 14.42 % Favored : 84.16 % 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 aren not related in a simple way. whole: 0.94 (0.24), residues: 1262 helix: 2.01 (0.21), residues: 644 sheet: 0.13 (0.47), residues: 119 loop : -1.14 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1313 TYR 0.016 0.001 TYR A 969 PHE 0.009 0.001 PHE A 712 TRP 0.015 0.001 TRP A 177 HIS 0.006 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00299 (13622) covalent geometry : angle 0.53422 (19105) hydrogen bonds : bond 0.04444 ( 587) hydrogen bonds : angle 3.88996 ( 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 82 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.381 Fit side-chains REVERT: A 175 ASP cc_start: 0.8260 (m-30) cc_final: 0.7944 (m-30) REVERT: A 969 TYR cc_start: 0.7867 (p90) cc_final: 0.7442 (p90) REVERT: A 972 MET cc_start: 0.8269 (mmp) cc_final: 0.7749 (mmm) REVERT: A 1006 MET cc_start: 0.7905 (ttp) cc_final: 0.7533 (ttp) REVERT: A 1061 ARG cc_start: 0.8269 (mtp180) cc_final: 0.7870 (mtp180) REVERT: A 1069 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: A 1239 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6465 (tt) REVERT: A 1285 GLN cc_start: 0.8370 (tt0) cc_final: 0.8102 (tt0) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.1357 time to fit residues: 15.4345 Evaluate side-chains 78 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1239 LEU 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: 0.9980 chunk 90 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3797 r_free = 0.3797 target = 0.114993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083327 restraints weight = 28433.592| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.67 r_work: 0.3110 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13622 Z= 0.131 Angle : 0.528 9.284 19105 Z= 0.281 Chirality : 0.034 0.298 2173 Planarity : 0.004 0.058 1929 Dihedral : 20.022 177.382 3463 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.32 % Rotamer: Outliers : 1.22 % Allowed : 14.72 % Favored : 84.06 % 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 aren not related in a simple way. whole: 0.99 (0.24), residues: 1262 helix: 2.05 (0.21), residues: 644 sheet: 0.13 (0.47), residues: 119 loop : -1.13 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1283 TYR 0.015 0.001 TYR A 969 PHE 0.009 0.001 PHE A 712 TRP 0.014 0.001 TRP A 177 HIS 0.006 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00285 (13622) covalent geometry : angle 0.52834 (19105) hydrogen bonds : bond 0.04326 ( 587) hydrogen bonds : angle 3.85345 ( 1609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3186.22 seconds wall clock time: 55 minutes 20.12 seconds (3320.12 seconds total)