Starting phenix.real_space_refine on Fri Jul 3 01:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eal_47835/07_2026/9eal_47835.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eal_47835/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9eal_47835/07_2026/9eal_47835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eal_47835/07_2026/9eal_47835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eal_47835/07_2026/9eal_47835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eal_47835/07_2026/9eal_47835.map" } 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-dev-6108/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: 3.02, per 1000 atoms: 0.26 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: 1.11 Conformation dependent library (CDL) restraints added in 481.0 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: 1.70 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: 3.47 Time building geometry restraints manager: 1.42 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: 16568 2.84 - 5.68: 271 5.68 - 8.51: 39 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=" 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 angle pdb=" O4 DT C 34 " pdb=" C4 DT C 34 " pdb=" C5 DT C 34 " ideal model delta sigma weight residual 124.90 121.70 3.20 7.00e-01 2.04e+00 2.09e+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: 1895 0.107 - 0.213: 112 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: 12.680 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.100 Find NCS groups from input model: 0.050 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- 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= 0.362 Angle : 0.922 14.190 16882 Z= 0.621 Chirality : 0.067 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 0.00529 / 0.36 (11952) covalent geometry : angle 0.92242 / 0.62 (16882) hydrogen bonds : bond 0.14176 / 13.93 ( 563) hydrogen bonds : angle 6.47676 / 7.75 ( 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 : 0.371 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: 0.4817 time to fit residues: 58.5928 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 : 0.381 ------------------------------------------------------------------------------- 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 = 0.147912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112618 restraints weight = 21150.452| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.21 r_work: 0.3475 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11952 Z= 0.151 Angle : 0.577 5.717 16882 Z= 0.335 Chirality : 0.042 0.256 2029 Planarity : 0.004 0.042 1639 Dihedral : 20.742 179.115 3193 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.50 % Allowed : 18.46 % Favored : 78.03 % 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: -0.43 (0.24), residues: 1148 helix: 0.33 (0.21), residues: 576 sheet: 0.28 (0.49), residues: 111 loop : -1.13 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 457 TYR 0.017 0.002 TYR A 656 PHE 0.022 0.002 PHE A 972 TRP 0.004 0.001 TRP A1074 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (11952) covalent geometry : angle 0.57675 / 0.34 (16882) hydrogen bonds : bond 0.05072 / 4.75 ( 563) hydrogen bonds : angle 4.90452 / 5.86 ( 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 : 0.451 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.8053 (mtp180) REVERT: A 314 LYS cc_start: 0.7539 (mmmm) cc_final: 0.6748 (ptpt) REVERT: A 575 PHE cc_start: 0.6133 (p90) cc_final: 0.5824 (p90) REVERT: A 746 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: A 951 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7022 (mtm110) REVERT: A 969 ASP cc_start: 0.7037 (t0) cc_final: 0.6818 (m-30) REVERT: A 976 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7588 (mtp-110) REVERT: A 1194 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7717 (mm) outliers start: 26 outliers final: 7 residues processed: 112 average time/residue: 0.4998 time to fit residues: 61.7719 Evaluate side-chains 92 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 25 optimal weight: 0.0980 chunk 97 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.144088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.107958 restraints weight = 21291.430| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.18 r_work: 0.3406 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1748 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= 0.157 Angle : 0.558 13.363 16882 Z= 0.318 Chirality : 0.041 0.235 2029 Planarity : 0.004 0.056 1639 Dihedral : 20.839 179.463 3193 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.50 % Allowed : 17.25 % Favored : 79.25 % 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: 0.03 (0.24), residues: 1148 helix: 0.82 (0.22), residues: 568 sheet: 0.07 (0.50), residues: 113 loop : -0.94 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 457 TYR 0.018 0.002 TYR A 656 PHE 0.026 0.002 PHE A 185 TRP 0.005 0.001 TRP A1074 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (11952) covalent geometry : angle 0.55822 / 0.32 (16882) hydrogen bonds : bond 0.04760 / 4.51 ( 563) hydrogen bonds : angle 4.55628 / 5.39 ( 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 122 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.382 Fit side-chains REVERT: A 314 LYS cc_start: 0.7585 (mmmm) cc_final: 0.6699 (ptpt) REVERT: A 481 VAL cc_start: 0.8905 (t) cc_final: 0.8701 (t) REVERT: A 942 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8619 (mmtm) REVERT: A 951 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7024 (mtm110) REVERT: A 968 LYS cc_start: 0.7891 (tmtt) cc_final: 0.7539 (tppp) REVERT: A 976 ARG cc_start: 0.8384 (mtt90) cc_final: 0.7846 (mtp-110) REVERT: A 1175 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6924 (mt-10) outliers start: 26 outliers final: 9 residues processed: 114 average time/residue: 0.4553 time to fit residues: 57.3485 Evaluate side-chains 99 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 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 1342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.140841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104517 restraints weight = 21100.866| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.15 r_work: 0.3361 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11952 Z= 0.160 Angle : 0.554 9.938 16882 Z= 0.315 Chirality : 0.041 0.242 2029 Planarity : 0.004 0.044 1639 Dihedral : 20.930 178.330 3193 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.23 % Allowed : 18.33 % Favored : 78.44 % 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: 0.24 (0.25), residues: 1148 helix: 0.97 (0.22), residues: 568 sheet: -0.02 (0.50), residues: 113 loop : -0.74 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 307 TYR 0.024 0.002 TYR A 973 PHE 0.024 0.002 PHE A 185 TRP 0.004 0.001 TRP A 18 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (11952) covalent geometry : angle 0.55363 / 0.31 (16882) hydrogen bonds : bond 0.04480 / 4.19 ( 563) hydrogen bonds : angle 4.41108 / 5.30 ( 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 121 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.378 Fit side-chains REVERT: A 80 CYS cc_start: 0.8365 (t) cc_final: 0.7059 (m) REVERT: A 84 GLU cc_start: 0.8200 (pt0) cc_final: 0.7962 (pm20) REVERT: A 314 LYS cc_start: 0.7563 (mmmm) cc_final: 0.6671 (ptpt) REVERT: A 321 MET cc_start: 0.8965 (mmt) cc_final: 0.8547 (mmt) REVERT: A 481 VAL cc_start: 0.8915 (t) cc_final: 0.8646 (t) REVERT: A 942 LYS cc_start: 0.9007 (tptm) cc_final: 0.8658 (mmtm) REVERT: A 951 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6995 (mtm110) REVERT: A 952 GLU cc_start: 0.7499 (pm20) cc_final: 0.7232 (pm20) REVERT: A 968 LYS cc_start: 0.7922 (tmtt) cc_final: 0.7534 (tppp) REVERT: A 976 ARG cc_start: 0.8505 (mtt90) cc_final: 0.7977 (mtp-110) REVERT: A 1194 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8228 (mm) REVERT: A 1237 TYR cc_start: 0.7035 (t80) cc_final: 0.6800 (t80) REVERT: A 1269 ILE cc_start: 0.7778 (mt) cc_final: 0.7563 (mt) REVERT: A 1344 ASP cc_start: 0.7901 (t0) cc_final: 0.7104 (p0) outliers start: 24 outliers final: 5 residues processed: 115 average time/residue: 0.4305 time to fit residues: 55.0310 Evaluate side-chains 94 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 951 ARG 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: 2.9990 chunk 118 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A1308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.134555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097426 restraints weight = 20780.790| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.13 r_work: 0.3250 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 11952 Z= 0.283 Angle : 0.651 9.455 16882 Z= 0.368 Chirality : 0.046 0.259 2029 Planarity : 0.005 0.047 1639 Dihedral : 21.112 177.345 3192 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.85 % Allowed : 18.87 % Favored : 76.28 % 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: 0.64 (0.22), residues: 578 sheet: -0.30 (0.48), residues: 113 loop : -0.72 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 307 TYR 0.026 0.002 TYR A 155 PHE 0.017 0.003 PHE A 105 TRP 0.007 0.001 TRP A 18 HIS 0.009 0.002 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.28 (11952) covalent geometry : angle 0.65118 / 0.37 (16882) hydrogen bonds : bond 0.05749 / 5.58 ( 563) hydrogen bonds : angle 4.68918 / 5.64 ( 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 115 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.364 Fit side-chains REVERT: A 80 CYS cc_start: 0.8478 (t) cc_final: 0.7791 (m) REVERT: A 314 LYS cc_start: 0.7768 (mmmm) cc_final: 0.6887 (ptpt) REVERT: A 481 VAL cc_start: 0.8967 (t) cc_final: 0.8726 (t) REVERT: A 942 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8678 (mmtm) REVERT: A 951 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7050 (mtm110) REVERT: A 968 LYS cc_start: 0.7977 (tmtt) cc_final: 0.7429 (tmmt) REVERT: A 976 ARG cc_start: 0.8568 (mtt90) cc_final: 0.8058 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8556 (t0) cc_final: 0.7985 (p0) outliers start: 36 outliers final: 15 residues processed: 103 average time/residue: 0.4427 time to fit residues: 50.2924 Evaluate side-chains 89 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 746 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1339 THR 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: 0.9980 chunk 30 optimal weight: 0.0030 chunk 33 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 125 optimal weight: 0.9990 chunk 80 optimal weight: 0.0020 chunk 20 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.137743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101196 restraints weight = 21065.927| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.12 r_work: 0.3312 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11952 Z= 0.123 Angle : 0.537 9.936 16882 Z= 0.304 Chirality : 0.040 0.255 2029 Planarity : 0.004 0.055 1639 Dihedral : 21.070 175.877 3192 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.56 % Allowed : 22.24 % 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: 0.33 (0.25), residues: 1148 helix: 1.02 (0.22), residues: 570 sheet: -0.26 (0.48), residues: 111 loop : -0.58 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 307 TYR 0.021 0.001 TYR A 155 PHE 0.017 0.001 PHE A 518 TRP 0.007 0.001 TRP A 18 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (11952) covalent geometry : angle 0.53723 / 0.30 (16882) hydrogen bonds : bond 0.04311 / 4.15 ( 563) hydrogen bonds : angle 4.38323 / 5.23 ( 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 93 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.273 Fit side-chains REVERT: A 80 CYS cc_start: 0.8466 (t) cc_final: 0.7053 (m) REVERT: A 84 GLU cc_start: 0.8230 (pt0) cc_final: 0.7828 (pm20) REVERT: A 314 LYS cc_start: 0.7614 (mmmm) cc_final: 0.6622 (ptpt) REVERT: A 321 MET cc_start: 0.8978 (mmt) cc_final: 0.8461 (mmt) REVERT: A 424 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7766 (mmt-90) REVERT: A 942 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8573 (mmtm) REVERT: A 951 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7181 (mtm110) REVERT: A 952 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: A 968 LYS cc_start: 0.7929 (tmtt) cc_final: 0.7600 (tppp) REVERT: A 976 ARG cc_start: 0.8521 (mtt90) cc_final: 0.8001 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8501 (t0) cc_final: 0.7936 (p0) outliers start: 19 outliers final: 7 residues processed: 88 average time/residue: 0.4982 time to fit residues: 48.1604 Evaluate side-chains 83 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 120 optimal weight: 0.0670 chunk 113 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.134137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097316 restraints weight = 20932.192| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.12 r_work: 0.3247 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11952 Z= 0.262 Angle : 0.612 9.799 16882 Z= 0.345 Chirality : 0.044 0.252 2029 Planarity : 0.004 0.053 1639 Dihedral : 21.086 174.986 3191 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.10 % Allowed : 21.97 % 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: 0.14 (0.25), residues: 1148 helix: 0.83 (0.22), residues: 579 sheet: -0.51 (0.47), residues: 113 loop : -0.59 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 307 TYR 0.023 0.002 TYR A 155 PHE 0.017 0.002 PHE A 970 TRP 0.007 0.001 TRP A 18 HIS 0.007 0.002 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.26 (11952) covalent geometry : angle 0.61186 / 0.34 (16882) hydrogen bonds : bond 0.05132 / 4.96 ( 563) hydrogen bonds : angle 4.50654 / 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 94 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.442 Fit side-chains REVERT: A 80 CYS cc_start: 0.8431 (t) cc_final: 0.7771 (m) REVERT: A 314 LYS cc_start: 0.7738 (mmmm) cc_final: 0.6826 (ptpt) REVERT: A 424 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7932 (mmt-90) REVERT: A 942 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8687 (mmtm) REVERT: A 951 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7193 (mtm110) REVERT: A 952 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: A 968 LYS cc_start: 0.7989 (tmtt) cc_final: 0.7455 (tmmt) REVERT: A 976 ARG cc_start: 0.8579 (mtt90) cc_final: 0.8109 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8713 (t0) cc_final: 0.8245 (p0) outliers start: 23 outliers final: 10 residues processed: 87 average time/residue: 0.4802 time to fit residues: 46.1703 Evaluate side-chains 82 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 424 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 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 1266 LEU 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: 0.5980 chunk 93 optimal weight: 0.5980 chunk 35 optimal weight: 40.0000 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.136464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100003 restraints weight = 20927.294| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.10 r_work: 0.3293 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11952 Z= 0.140 Angle : 0.540 10.968 16882 Z= 0.305 Chirality : 0.040 0.258 2029 Planarity : 0.004 0.061 1639 Dihedral : 21.049 173.835 3191 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.70 % Allowed : 22.37 % 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: 0.41 (0.25), residues: 1148 helix: 1.09 (0.22), residues: 570 sheet: -0.43 (0.49), residues: 111 loop : -0.48 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 307 TYR 0.020 0.001 TYR A 155 PHE 0.018 0.001 PHE A 518 TRP 0.008 0.001 TRP A 18 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (11952) covalent geometry : angle 0.53991 / 0.30 (16882) hydrogen bonds : bond 0.04232 / 4.07 ( 563) hydrogen bonds : angle 4.32045 / 5.13 ( 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 89 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.385 Fit side-chains REVERT: A 80 CYS cc_start: 0.8447 (t) cc_final: 0.7010 (m) REVERT: A 84 GLU cc_start: 0.8186 (pt0) cc_final: 0.7757 (pm20) REVERT: A 321 MET cc_start: 0.9000 (mmt) cc_final: 0.8480 (mmt) REVERT: A 424 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7786 (mmt-90) REVERT: A 481 VAL cc_start: 0.9012 (t) cc_final: 0.8794 (t) REVERT: A 942 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8637 (mmtm) REVERT: A 952 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: A 968 LYS cc_start: 0.7953 (tmtt) cc_final: 0.7606 (tppp) REVERT: A 976 ARG cc_start: 0.8562 (mtt90) cc_final: 0.8042 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8617 (t0) cc_final: 0.8166 (p0) outliers start: 20 outliers final: 11 residues processed: 85 average time/residue: 0.4990 time to fit residues: 46.6763 Evaluate side-chains 81 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 424 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 745 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 942 LYS 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 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.5980 chunk 35 optimal weight: 40.0000 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 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: 1.9990 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.135901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099377 restraints weight = 20769.334| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.09 r_work: 0.3282 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11952 Z= 0.173 Angle : 0.555 13.027 16882 Z= 0.312 Chirality : 0.041 0.257 2029 Planarity : 0.004 0.066 1639 Dihedral : 21.029 173.447 3191 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.56 % Allowed : 22.78 % Favored : 74.66 % 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: 1.03 (0.22), residues: 577 sheet: -0.48 (0.48), residues: 113 loop : -0.50 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 307 TYR 0.019 0.001 TYR A 155 PHE 0.013 0.001 PHE A1080 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 0.00365 / 0.17 (11952) covalent geometry : angle 0.55532 / 0.31 (16882) hydrogen bonds : bond 0.04311 / 4.16 ( 563) hydrogen bonds : angle 4.31033 / 5.13 ( 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 88 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.363 Fit side-chains REVERT: A 80 CYS cc_start: 0.8454 (t) cc_final: 0.7044 (m) REVERT: A 84 GLU cc_start: 0.8193 (pt0) cc_final: 0.7783 (pm20) REVERT: A 321 MET cc_start: 0.9010 (mmt) cc_final: 0.8446 (mmt) REVERT: A 424 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7821 (mmt-90) REVERT: A 481 VAL cc_start: 0.9013 (t) cc_final: 0.8794 (t) REVERT: A 942 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8636 (mmtm) REVERT: A 951 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7167 (mtm110) REVERT: A 952 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: A 968 LYS cc_start: 0.7937 (tmtt) cc_final: 0.7610 (tppp) REVERT: A 976 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8022 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8629 (t0) cc_final: 0.8194 (p0) outliers start: 19 outliers final: 11 residues processed: 84 average time/residue: 0.4826 time to fit residues: 44.6707 Evaluate side-chains 83 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 424 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 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 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.136779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.100354 restraints weight = 20931.381| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.10 r_work: 0.3297 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11952 Z= 0.145 Angle : 0.531 11.442 16882 Z= 0.299 Chirality : 0.039 0.261 2029 Planarity : 0.004 0.057 1639 Dihedral : 20.972 172.089 3191 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.16 % Allowed : 23.05 % Favored : 74.80 % 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: 0.55 (0.25), residues: 1148 helix: 1.20 (0.22), residues: 572 sheet: -0.40 (0.49), residues: 111 loop : -0.39 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 307 TYR 0.018 0.001 TYR A 155 PHE 0.020 0.001 PHE A 518 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 0.00296 / 0.14 (11952) covalent geometry : angle 0.53066 / 0.30 (16882) hydrogen bonds : bond 0.04005 / 3.88 ( 563) hydrogen bonds : angle 4.20392 / 4.98 ( 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 85 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.330 Fit side-chains REVERT: A 80 CYS cc_start: 0.8447 (t) cc_final: 0.7025 (m) REVERT: A 84 GLU cc_start: 0.8144 (pt0) cc_final: 0.7719 (pm20) REVERT: A 321 MET cc_start: 0.8989 (mmt) cc_final: 0.8490 (mmt) REVERT: A 424 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7804 (mmt-90) REVERT: A 481 VAL cc_start: 0.8962 (t) cc_final: 0.8733 (t) REVERT: A 942 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8625 (mmtm) REVERT: A 952 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: A 968 LYS cc_start: 0.7924 (tmtt) cc_final: 0.7602 (tppp) REVERT: A 976 ARG cc_start: 0.8523 (mtt90) cc_final: 0.7992 (mtp-110) REVERT: A 1344 ASP cc_start: 0.8626 (t0) cc_final: 0.8195 (p0) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.4785 time to fit residues: 43.2579 Evaluate side-chains 77 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 424 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 746 GLU Chi-restraints excluded: chain A residue 942 LYS 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 1266 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 117 optimal weight: 0.0870 chunk 86 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.136523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100185 restraints weight = 20852.230| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.10 r_work: 0.3296 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3690 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= 0.142 Angle : 0.534 11.844 16882 Z= 0.301 Chirality : 0.039 0.260 2029 Planarity : 0.004 0.065 1639 Dihedral : 20.952 171.428 3191 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.16 % Allowed : 23.85 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.24 (0.22), residues: 573 sheet: -0.47 (0.48), residues: 113 loop : -0.37 (0.30), residues: 462 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 0.012 0.001 PHE A 970 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 0.00290 / 0.14 (11952) covalent geometry : angle 0.53438 / 0.30 (16882) hydrogen bonds : bond 0.03977 / 3.86 ( 563) hydrogen bonds : angle 4.16251 / 4.94 ( 1525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4015.17 seconds wall clock time: 69 minutes 12.94 seconds (4152.94 seconds total)