Starting phenix.real_space_refine on Wed Aug 5 19:17:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eal_47835/08_2026/9eal_47835.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eal_47835/08_2026/9eal_47835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eal_47835/08_2026/9eal_47835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eal_47835/08_2026/9eal_47835.map" model { file = "/net/cci-nas-00/data/ceres_data/9eal_47835/08_2026/9eal_47835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eal_47835/08_2026/9eal_47835.cif" } resolution = 2.83 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= 0.010 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: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 16 5.16 5 C 6763 2.51 5 N 2039 2.21 5 O 2477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s 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: 11438 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2038 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 83} Chain: "C" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 648 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 8420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 8420 Classifications: {'peptide': 1156} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 31, 'TRANS': 1124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1025 Unresolved non-hydrogen angles: 1261 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'ASP:plan': 37, 'GLU:plan': 46, 'ASN:plan1': 22, 'GLN:plan1': 18, 'ARG:plan': 13, 'PHE:plan': 13, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 580 Time building chain proxies: 2.38, per 1000 atoms: 0.21 Number of scatterers: 11438 At special positions: 0 Unit cell: (85.8196, 135.812, 122.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 143 15.00 O 2477 8.00 N 2039 7.00 C 6763 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: 0.80 Conformation dependent library (CDL) restraints added in 429.6 milliseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 54.8% alpha, 7.3% beta 52 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.618A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.781A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.754A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 195 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 286 through 306 removed outlier: 4.531A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.997A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.884A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.790A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 527 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.606A pdb=" N GLU A 573 " --> pdb=" O PHE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.857A pdb=" N TYR A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 643 removed outlier: 3.578A pdb=" N PHE A 643 " --> pdb=" O ALA A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.519A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 701 through 714 removed outlier: 3.876A pdb=" N LYS A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.509A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.529A pdb=" N SER A 964 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.422A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR A 995 " --> pdb=" O ALA A 991 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 4.183A pdb=" N PHE A1045 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.486A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.658A pdb=" N LEU A1194 " --> pdb=" O LYS A1191 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1191 through 1195' Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 removed outlier: 3.545A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.651A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.502A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1344 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.114A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 1050 through 1051 Processing sheet with id=AA4, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 3.780A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.586A pdb=" N PHE A1134 " --> pdb=" O ILE A1120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.533A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1219 through 1222 removed outlier: 3.720A pdb=" N GLU A1219 " --> pdb=" O SER A1216 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN A1221 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU A1214 " --> pdb=" O GLN A1221 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1325 437 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.11 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: 2441 1.33 - 1.45: 3308 1.45 - 1.57: 5890 1.57 - 1.69: 283 1.69 - 1.81: 30 Bond restraints: 11952 Sorted by residual: bond pdb=" C1' DC C 29 " pdb=" N1 DC C 29 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" C3' DC C 7 " pdb=" O3' DC C 7 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" C3' DG D 38 " pdb=" C2' DG D 38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC D 44 " pdb=" C2' DC D 44 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.476 -0.041 1.30e-02 5.92e+03 1.01e+01 ... (remaining 11947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 16563 2.84 - 5.68: 275 5.68 - 8.51: 40 8.51 - 11.35: 3 11.35 - 14.19: 1 Bond angle restraints: 16882 Sorted by residual: angle pdb=" O4' DC C 26 " pdb=" C4' DC C 26 " pdb=" C3' DC C 26 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.81e+01 angle pdb=" C3' A B 68 " pdb=" O3' A B 68 " pdb=" P A B 69 " ideal model delta sigma weight residual 119.70 125.48 -5.78 1.20e+00 6.94e-01 2.32e+01 angle pdb=" N3 DT C 34 " pdb=" C4 DT C 34 " pdb=" O4 DT C 34 " ideal model delta sigma weight residual 119.90 122.77 -2.87 6.00e-01 2.78e+00 2.28e+01 angle pdb=" CB MET A 648 " pdb=" CG MET A 648 " pdb=" SD MET A 648 " ideal model delta sigma weight residual 112.70 126.89 -14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" C ASP A 628 " pdb=" N ARG A 629 " pdb=" CA ARG A 629 " ideal model delta sigma weight residual 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.23e+01 ... (remaining 16877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 6640 35.30 - 70.60: 431 70.60 - 105.90: 24 105.90 - 141.20: 1 141.20 - 176.50: 4 Dihedral angle restraints: 7100 sinusoidal: 3708 harmonic: 3392 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 31.47 168.53 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" CA VAL A1092 " pdb=" C VAL A1092 " pdb=" N ASN A1093 " pdb=" CA ASN A1093 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" O4' G B 5 " pdb=" C1' G B 5 " pdb=" N9 G B 5 " pdb=" C4 G B 5 " ideal model delta sinusoidal sigma weight residual 70.00 -3.39 73.39 1 2.00e+01 2.50e-03 1.71e+01 ... (remaining 7097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1837 0.107 - 0.213: 170 0.213 - 0.320: 5 0.320 - 0.427: 3 0.427 - 0.533: 14 Chirality restraints: 2029 Sorted by residual: chirality pdb=" P A B 69 " pdb=" OP1 A B 69 " pdb=" OP2 A B 69 " pdb=" O5' A B 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" P A B 68 " pdb=" OP1 A B 68 " pdb=" OP2 A B 68 " pdb=" O5' A B 68 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" P A B 17 " pdb=" OP1 A B 17 " pdb=" OP2 A B 17 " pdb=" O5' A B 17 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.58e+00 ... (remaining 2026 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 976 " 0.547 9.50e-02 1.11e+02 2.45e-01 3.69e+01 pdb=" NE ARG A 976 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 976 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 976 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 976 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 967 " 0.412 9.50e-02 1.11e+02 1.84e-01 2.09e+01 pdb=" NE ARG A 967 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 967 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 967 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 967 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 518 " 0.014 2.00e-02 2.50e+03 2.20e-02 8.44e+00 pdb=" CG PHE A 518 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 518 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 518 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 518 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 518 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 518 " -0.001 2.00e-02 2.50e+03 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1465 2.76 - 3.29: 10575 3.29 - 3.83: 21144 3.83 - 4.36: 24714 4.36 - 4.90: 37834 Nonbonded interactions: 95732 Sorted by model distance: nonbonded pdb=" O2' A B 47 " pdb=" O LEU A 101 " model vdw 2.220 3.040 nonbonded pdb=" O ILE A1273 " pdb=" OG SER A1277 " model vdw 2.267 3.040 nonbonded pdb=" O LEU A 380 " pdb=" OG1 THR A 386 " model vdw 2.293 3.040 nonbonded pdb=" O TYR A 521 " pdb=" OG1 THR A 525 " model vdw 2.306 3.040 nonbonded pdb=" OE1 GLN A1305 " pdb=" OH TYR A1326 " model vdw 2.343 3.040 ... (remaining 95727 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: 10.910 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11952 Z= 0.372 Angle : 0.957 14.190 16882 Z= 0.661 Chirality : 0.071 0.533 2029 Planarity : 0.010 0.245 1639 Dihedral : 19.858 176.496 4902 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.81 % Allowed : 22.10 % Favored : 77.09 % 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: -1.36 (0.23), residues: 1148 helix: -0.70 (0.20), residues: 580 sheet: 0.48 (0.53), residues: 96 loop : -1.32 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 457 TYR 0.036 0.002 TYR A 155 PHE 0.050 0.003 PHE A 518 TRP 0.015 0.002 TRP A1074 HIS 0.008 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.37 (11952) covalent geometry : angle 0.95727 / 0.66 (16882) hydrogen bonds : bond 0.14176 / 15.52 ( 563) hydrogen bonds : angle 6.47676 / 8.08 ( 1525) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.360 Fit side-chains REVERT: A 314 LYS cc_start: 0.7663 (mmmm) cc_final: 0.6822 (ptmt) REVERT: A 575 PHE cc_start: 0.6077 (p90) cc_final: 0.5764 (p90) REVERT: A 951 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7434 (mtm-85) REVERT: A 1125 ASP cc_start: 0.7609 (p0) cc_final: 0.7402 (p0) REVERT: A 1344 ASP cc_start: 0.6694 (t0) cc_final: 0.6192 (p0) outliers start: 6 outliers final: 2 residues processed: 110 average time/residue: 0.3792 time to fit residues: 46.0790 Evaluate side-chains 90 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0060 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS A 983 HIS A1115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.148035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112665 restraints weight = 21135.226| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.22 r_work: 0.3476 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11952 Z= 0.147 Angle : 0.582 7.925 16882 Z= 0.334 Chirality : 0.042 0.246 2029 Planarity : 0.005 0.048 1639 Dihedral : 20.679 179.728 3193 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.50 % Allowed : 18.60 % Favored : 77.90 % 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: -0.40 (0.24), residues: 1148 helix: 0.36 (0.21), residues: 576 sheet: 0.26 (0.50), residues: 111 loop : -1.13 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 654 TYR 0.038 0.002 TYR A 656 PHE 0.022 0.002 PHE A 972 TRP 0.004 0.001 TRP A1074 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (11952) covalent geometry : angle 0.58207 / 0.33 (16882) hydrogen bonds : bond 0.05144 / 5.38 ( 563) hydrogen bonds : angle 4.91484 / 6.18 ( 1525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.329 Fit side-chains REVERT: A 307 ARG cc_start: 0.8442 (mtp-110) cc_final: 0.8087 (mtp180) REVERT: A 314 LYS cc_start: 0.7547 (mmmm) cc_final: 0.6757 (ptpt) REVERT: A 575 PHE cc_start: 0.6135 (p90) cc_final: 0.5824 (p90) REVERT: A 746 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: A 951 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7012 (mtm110) REVERT: A 969 ASP cc_start: 0.7051 (t0) cc_final: 0.6831 (m-30) REVERT: A 976 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7576 (mtp-110) REVERT: A 1194 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7728 (mm) outliers start: 26 outliers final: 7 residues processed: 112 average time/residue: 0.4333 time to fit residues: 53.6825 Evaluate side-chains 91 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 25 optimal weight: 0.1980 chunk 97 optimal weight: 9.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 GLN A1317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.142191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105824 restraints weight = 21224.359| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.17 r_work: 0.3377 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11952 Z= 0.163 Angle : 0.589 13.784 16882 Z= 0.329 Chirality : 0.042 0.263 2029 Planarity : 0.005 0.075 1639 Dihedral : 20.822 178.671 3193 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.37 % Allowed : 18.46 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.24), residues: 1148 helix: 0.71 (0.21), residues: 563 sheet: 0.04 (0.49), residues: 113 loop : -0.91 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.016 0.001 TYR A 155 PHE 0.030 0.002 PHE A 185 TRP 0.005 0.001 TRP A1074 HIS 0.006 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (11952) covalent geometry : angle 0.58863 / 0.33 (16882) hydrogen bonds : bond 0.04968 / 5.21 ( 563) hydrogen bonds : angle 4.56638 / 5.69 ( 1525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.437 Fit side-chains REVERT: A 314 LYS cc_start: 0.7594 (mmmm) cc_final: 0.6715 (ptpt) REVERT: A 481 VAL cc_start: 0.8911 (t) cc_final: 0.8697 (t) REVERT: A 942 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8623 (mmtm) REVERT: A 951 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7016 (mtm110) REVERT: A 968 LYS cc_start: 0.7898 (tmtt) cc_final: 0.7558 (tppp) REVERT: A 976 ARG cc_start: 0.8445 (mtt90) cc_final: 0.7940 (mtp-110) REVERT: A 1175 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6987 (mt-10) outliers start: 25 outliers final: 10 residues processed: 119 average time/residue: 0.3957 time to fit residues: 52.2156 Evaluate side-chains 99 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.137544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100686 restraints weight = 21008.914| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.12 r_work: 0.3303 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11952 Z= 0.214 Angle : 0.614 8.563 16882 Z= 0.340 Chirality : 0.044 0.272 2029 Planarity : 0.004 0.043 1639 Dihedral : 20.978 178.642 3193 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.37 % Allowed : 19.81 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.25), residues: 1148 helix: 0.81 (0.22), residues: 574 sheet: -0.23 (0.49), residues: 113 loop : -0.80 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 307 TYR 0.025 0.002 TYR A 973 PHE 0.024 0.002 PHE A1080 TRP 0.005 0.001 TRP A 18 HIS 0.006 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (11952) covalent geometry : angle 0.61399 / 0.34 (16882) hydrogen bonds : bond 0.05021 / 5.33 ( 563) hydrogen bonds : angle 4.56483 / 5.76 ( 1525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.338 Fit side-chains REVERT: A 80 CYS cc_start: 0.8410 (t) cc_final: 0.7773 (m) REVERT: A 307 ARG cc_start: 0.8357 (mtp-110) cc_final: 0.7941 (mtp180) REVERT: A 314 LYS cc_start: 0.7672 (mmmm) cc_final: 0.6764 (ptpt) REVERT: A 481 VAL cc_start: 0.8955 (t) cc_final: 0.8706 (t) REVERT: A 942 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8661 (mmtm) REVERT: A 951 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7003 (mtm110) REVERT: A 952 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: A 968 LYS cc_start: 0.7953 (tmtt) cc_final: 0.7559 (tppp) REVERT: A 976 ARG cc_start: 0.8556 (mtt90) cc_final: 0.8026 (mtp-110) REVERT: A 1194 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 1237 TYR cc_start: 0.7334 (t80) cc_final: 0.6957 (t80) REVERT: A 1344 ASP cc_start: 0.8278 (t0) cc_final: 0.7549 (p0) outliers start: 25 outliers final: 9 residues processed: 104 average time/residue: 0.4400 time to fit residues: 50.3138 Evaluate side-chains 93 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 77 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102035 restraints weight = 20801.481| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.12 r_work: 0.3327 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11952 Z= 0.141 Angle : 0.545 9.637 16882 Z= 0.306 Chirality : 0.040 0.263 2029 Planarity : 0.004 0.040 1639 Dihedral : 20.959 178.408 3192 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.37 % Allowed : 20.62 % Favored : 76.01 % 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: 0.35 (0.25), residues: 1148 helix: 1.08 (0.22), residues: 569 sheet: -0.23 (0.48), residues: 113 loop : -0.63 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 461 TYR 0.019 0.001 TYR A 155 PHE 0.021 0.001 PHE A 185 TRP 0.007 0.001 TRP A 18 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (11952) covalent geometry : angle 0.54510 / 0.31 (16882) hydrogen bonds : bond 0.04382 / 4.60 ( 563) hydrogen bonds : angle 4.39349 / 5.53 ( 1525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.415 Fit side-chains REVERT: A 80 CYS cc_start: 0.8376 (t) cc_final: 0.7726 (m) REVERT: A 314 LYS cc_start: 0.7598 (mmmm) cc_final: 0.6692 (ptpt) REVERT: A 424 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7773 (mmt-90) REVERT: A 942 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8612 (mmtm) REVERT: A 968 LYS cc_start: 0.7941 (tmtt) cc_final: 0.7599 (tppp) REVERT: A 976 ARG cc_start: 0.8483 (mtt90) cc_final: 0.7981 (mtp-110) REVERT: A 1194 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8385 (mm) REVERT: A 1344 ASP cc_start: 0.8322 (t0) cc_final: 0.7685 (p0) outliers start: 25 outliers final: 12 residues processed: 97 average time/residue: 0.4754 time to fit residues: 50.7980 Evaluate side-chains 91 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 30 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102168 restraints weight = 21040.673| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.13 r_work: 0.3327 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11952 Z= 0.135 Angle : 0.541 9.474 16882 Z= 0.302 Chirality : 0.040 0.265 2029 Planarity : 0.003 0.048 1639 Dihedral : 20.940 177.551 3192 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.70 % Allowed : 21.43 % Favored : 75.88 % 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: 0.41 (0.25), residues: 1148 helix: 1.13 (0.22), residues: 568 sheet: -0.20 (0.48), residues: 113 loop : -0.59 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 307 TYR 0.018 0.001 TYR A 155 PHE 0.016 0.001 PHE A 518 TRP 0.006 0.001 TRP A 18 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (11952) covalent geometry : angle 0.54065 / 0.30 (16882) hydrogen bonds : bond 0.04257 / 4.48 ( 563) hydrogen bonds : angle 4.33711 / 5.43 ( 1525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.295 Fit side-chains REVERT: A 80 CYS cc_start: 0.8359 (t) cc_final: 0.6962 (m) REVERT: A 84 GLU cc_start: 0.8188 (pt0) cc_final: 0.7838 (pm20) REVERT: A 314 LYS cc_start: 0.7582 (mmmm) cc_final: 0.6688 (ptpt) REVERT: A 317 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8409 (tp) REVERT: A 321 MET cc_start: 0.8963 (mmt) cc_final: 0.8513 (mmt) REVERT: A 424 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7798 (mmt-90) REVERT: A 942 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8612 (mmtm) REVERT: A 951 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7089 (mtm110) REVERT: A 968 LYS cc_start: 0.7950 (tmtt) cc_final: 0.7629 (tppp) REVERT: A 976 ARG cc_start: 0.8502 (mtt90) cc_final: 0.7971 (mtp-110) REVERT: A 1194 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8440 (mm) REVERT: A 1237 TYR cc_start: 0.7396 (t80) cc_final: 0.7130 (t80) REVERT: A 1344 ASP cc_start: 0.8336 (t0) cc_final: 0.7687 (p0) outliers start: 20 outliers final: 11 residues processed: 88 average time/residue: 0.4967 time to fit residues: 48.0878 Evaluate side-chains 92 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.137000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100314 restraints weight = 20872.353| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.12 r_work: 0.3295 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11952 Z= 0.165 Angle : 0.560 9.264 16882 Z= 0.311 Chirality : 0.041 0.269 2029 Planarity : 0.004 0.050 1639 Dihedral : 20.961 176.671 3192 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.77 % Allowed : 20.49 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.36 (0.25), residues: 1148 helix: 1.02 (0.22), residues: 578 sheet: -0.28 (0.48), residues: 113 loop : -0.53 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 307 TYR 0.020 0.001 TYR A 155 PHE 0.009 0.001 PHE A 478 TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (11952) covalent geometry : angle 0.55984 / 0.31 (16882) hydrogen bonds : bond 0.04421 / 4.68 ( 563) hydrogen bonds : angle 4.29794 / 5.39 ( 1525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.242 Fit side-chains REVERT: A 80 CYS cc_start: 0.8405 (t) cc_final: 0.7736 (m) REVERT: A 314 LYS cc_start: 0.7623 (mmmm) cc_final: 0.6697 (ptpt) REVERT: A 317 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 321 MET cc_start: 0.9002 (mmt) cc_final: 0.8481 (mmt) REVERT: A 619 ILE cc_start: 0.8344 (mm) cc_final: 0.8125 (mp) REVERT: A 942 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8645 (mmtm) REVERT: A 951 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7090 (mtm110) REVERT: A 968 LYS cc_start: 0.7966 (tmtt) cc_final: 0.7616 (tppp) REVERT: A 976 ARG cc_start: 0.8508 (mtt90) cc_final: 0.7987 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8486 (t0) cc_final: 0.7875 (p0) outliers start: 28 outliers final: 13 residues processed: 97 average time/residue: 0.3863 time to fit residues: 41.6309 Evaluate side-chains 89 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.136270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099643 restraints weight = 20872.138| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.10 r_work: 0.3283 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11952 Z= 0.175 Angle : 0.569 9.363 16882 Z= 0.316 Chirality : 0.041 0.274 2029 Planarity : 0.004 0.055 1639 Dihedral : 20.994 175.409 3192 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.10 % Allowed : 21.70 % Favored : 75.20 % 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: 0.45 (0.25), residues: 1148 helix: 1.07 (0.22), residues: 578 sheet: -0.29 (0.49), residues: 111 loop : -0.44 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 307 TYR 0.020 0.001 TYR A 155 PHE 0.016 0.001 PHE A 518 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (11952) covalent geometry : angle 0.56945 / 0.32 (16882) hydrogen bonds : bond 0.04411 / 4.69 ( 563) hydrogen bonds : angle 4.30661 / 5.38 ( 1525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.362 Fit side-chains REVERT: A 80 CYS cc_start: 0.8504 (t) cc_final: 0.7186 (m) REVERT: A 84 GLU cc_start: 0.8267 (pt0) cc_final: 0.7906 (pm20) REVERT: A 314 LYS cc_start: 0.7634 (mmmm) cc_final: 0.6709 (ptpt) REVERT: A 317 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8386 (tp) REVERT: A 321 MET cc_start: 0.9026 (mmt) cc_final: 0.8508 (mmt) REVERT: A 424 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7791 (mmt-90) REVERT: A 619 ILE cc_start: 0.8339 (mm) cc_final: 0.8106 (mp) REVERT: A 942 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8651 (mmtm) REVERT: A 951 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7124 (mtm110) REVERT: A 952 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: A 968 LYS cc_start: 0.7974 (tmtt) cc_final: 0.7622 (tppp) REVERT: A 976 ARG cc_start: 0.8523 (mtt90) cc_final: 0.7981 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8050 (p0) outliers start: 23 outliers final: 10 residues processed: 82 average time/residue: 0.4849 time to fit residues: 43.7735 Evaluate side-chains 82 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1344 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.9980 chunk 35 optimal weight: 40.0000 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 0.0020 chunk 114 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.136642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.100285 restraints weight = 20737.404| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.08 r_work: 0.3296 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11952 Z= 0.147 Angle : 0.553 13.208 16882 Z= 0.305 Chirality : 0.040 0.274 2029 Planarity : 0.004 0.062 1639 Dihedral : 20.969 174.782 3191 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.43 % Allowed : 22.24 % Favored : 75.34 % 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: 0.53 (0.25), residues: 1148 helix: 1.14 (0.22), residues: 578 sheet: -0.27 (0.49), residues: 111 loop : -0.40 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 307 TYR 0.019 0.001 TYR A 155 PHE 0.008 0.001 PHE A 478 TRP 0.007 0.001 TRP A 18 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (11952) covalent geometry : angle 0.55290 / 0.31 (16882) hydrogen bonds : bond 0.04187 / 4.46 ( 563) hydrogen bonds : angle 4.24674 / 5.29 ( 1525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.244 Fit side-chains REVERT: A 80 CYS cc_start: 0.8441 (t) cc_final: 0.7014 (m) REVERT: A 84 GLU cc_start: 0.8185 (pt0) cc_final: 0.7769 (pm20) REVERT: A 317 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8360 (tp) REVERT: A 321 MET cc_start: 0.9003 (mmt) cc_final: 0.8536 (mmt) REVERT: A 424 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7766 (mmt-90) REVERT: A 481 VAL cc_start: 0.8995 (t) cc_final: 0.8769 (t) REVERT: A 619 ILE cc_start: 0.8353 (mm) cc_final: 0.8118 (mp) REVERT: A 942 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8644 (mmtm) REVERT: A 951 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7115 (mtm110) REVERT: A 952 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: A 968 LYS cc_start: 0.7957 (tmtt) cc_final: 0.7609 (tppp) REVERT: A 976 ARG cc_start: 0.8488 (mtt90) cc_final: 0.7974 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8131 (p0) outliers start: 18 outliers final: 12 residues processed: 85 average time/residue: 0.4540 time to fit residues: 42.7100 Evaluate side-chains 83 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1344 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 0.0000 chunk 72 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.136918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100522 restraints weight = 20883.166| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.10 r_work: 0.3299 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11952 Z= 0.132 Angle : 0.539 12.234 16882 Z= 0.300 Chirality : 0.039 0.275 2029 Planarity : 0.004 0.064 1639 Dihedral : 20.953 174.614 3191 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.29 % Allowed : 22.78 % Favored : 74.93 % 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: 0.59 (0.25), residues: 1148 helix: 1.20 (0.22), residues: 578 sheet: -0.28 (0.49), residues: 111 loop : -0.38 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 307 TYR 0.018 0.001 TYR A 155 PHE 0.019 0.001 PHE A 518 TRP 0.006 0.001 TRP A 18 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (11952) covalent geometry : angle 0.53890 / 0.30 (16882) hydrogen bonds : bond 0.04084 / 4.35 ( 563) hydrogen bonds : angle 4.20803 / 5.24 ( 1525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.398 Fit side-chains REVERT: A 80 CYS cc_start: 0.8457 (t) cc_final: 0.7036 (m) REVERT: A 84 GLU cc_start: 0.8195 (pt0) cc_final: 0.7757 (pm20) REVERT: A 317 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8366 (tp) REVERT: A 321 MET cc_start: 0.8996 (mmt) cc_final: 0.8535 (mmt) REVERT: A 424 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7776 (mmt-90) REVERT: A 481 VAL cc_start: 0.9036 (t) cc_final: 0.8805 (t) REVERT: A 619 ILE cc_start: 0.8337 (mm) cc_final: 0.8103 (mp) REVERT: A 942 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8646 (mmtm) REVERT: A 951 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7146 (mtm110) REVERT: A 952 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: A 968 LYS cc_start: 0.7957 (tmtt) cc_final: 0.7590 (tppp) REVERT: A 976 ARG cc_start: 0.8504 (mtt90) cc_final: 0.7967 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8138 (p0) outliers start: 17 outliers final: 11 residues processed: 78 average time/residue: 0.4874 time to fit residues: 42.1642 Evaluate side-chains 80 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1344 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 0.0870 chunk 69 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.136109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099478 restraints weight = 20859.191| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.09 r_work: 0.3286 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11952 Z= 0.159 Angle : 0.558 13.749 16882 Z= 0.307 Chirality : 0.041 0.276 2029 Planarity : 0.004 0.060 1639 Dihedral : 20.947 174.027 3191 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.16 % Allowed : 22.78 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.60 (0.25), residues: 1148 helix: 1.21 (0.22), residues: 581 sheet: -0.37 (0.48), residues: 113 loop : -0.36 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 307 TYR 0.020 0.001 TYR A 155 PHE 0.012 0.001 PHE A1080 TRP 0.006 0.001 TRP A 18 HIS 0.004 0.001 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (11952) covalent geometry : angle 0.55794 / 0.31 (16882) hydrogen bonds : bond 0.04193 / 4.48 ( 563) hydrogen bonds : angle 4.22514 / 5.27 ( 1525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3866.34 seconds wall clock time: 66 minutes 29.39 seconds (3989.39 seconds total)