Starting phenix.real_space_refine on Wed Aug 5 23:44:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7q_65730/08_2026/9w7q_65730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7q_65730/08_2026/9w7q_65730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w7q_65730/08_2026/9w7q_65730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7q_65730/08_2026/9w7q_65730.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w7q_65730/08_2026/9w7q_65730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7q_65730/08_2026/9w7q_65730.map" } resolution = 3.79 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= 0.006 sd= 0.044 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 135 5.49 5 S 19 5.16 5 C 7195 2.51 5 N 2128 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 12105 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9201 Classifications: {'peptide': 1129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1098} Chain breaks: 2 Chain: "B" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 618 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1981 Classifications: {'RNA': 93} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 37} Link IDs: {'rna2p': 11, 'rna3p': 81} Time building chain proxies: 1.94, per 1000 atoms: 0.16 Number of scatterers: 12105 At special positions: 0 Unit cell: (134.75, 104.566, 144.452, 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 19 16.00 P 135 15.00 O 2628 8.00 N 2128 7.00 C 7195 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: 0.85 Conformation dependent library (CDL) restraints added in 390.4 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 56.2% alpha, 8.0% beta 52 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.769A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.781A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.546A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 4.037A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.528A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 removed outlier: 4.369A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 307 removed outlier: 3.649A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.725A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 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 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.223A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.063A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.705A 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 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.580A pdb=" N GLN A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.120A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.538A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.627A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.665A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.071A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 4.437A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (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 1170 through 1177 removed outlier: 3.517A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix 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 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.596A 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 Processing helix chain 'A' and resid 1314 through 1317 removed outlier: 3.604A pdb=" N ASN A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1317' Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.768A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) 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: 4.250A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 7 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 760 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.475A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 942 through 943 removed outlier: 4.706A pdb=" N LYS A 942 " --> pdb=" O ILE A 950 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.625A pdb=" N ALA A1147 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.709A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 260 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 1.16 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: 2639 1.33 - 1.45: 3274 1.45 - 1.57: 6400 1.57 - 1.69: 270 1.69 - 1.81: 36 Bond restraints: 12619 Sorted by residual: bond pdb=" C3' DT B 10 " pdb=" C2' DT B 10 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" C3' DA B 27 " pdb=" C2' DA B 27 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DA C 13 " pdb=" C2' DA C 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C4' DA B 24 " pdb=" C3' DA B 24 " ideal model delta sigma weight residual 1.529 1.501 0.028 1.00e-02 1.00e+04 7.61e+00 ... (remaining 12614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 16544 1.40 - 2.79: 966 2.79 - 4.19: 116 4.19 - 5.58: 13 5.58 - 6.98: 1 Bond angle restraints: 17640 Sorted by residual: angle pdb=" O4' DG B 18 " pdb=" C4' DG B 18 " pdb=" C3' DG B 18 " ideal model delta sigma weight residual 106.00 102.61 3.39 6.00e-01 2.78e+00 3.20e+01 angle pdb=" O4' DG B 23 " pdb=" C4' DG B 23 " pdb=" C3' DG B 23 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" O4' DA B 22 " pdb=" C4' DA B 22 " pdb=" C3' DA B 22 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT B 19 " pdb=" C4 DT B 19 " pdb=" O4 DT B 19 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 17635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 6750 17.25 - 34.50: 538 34.50 - 51.75: 192 51.75 - 69.00: 141 69.00 - 86.25: 25 Dihedral angle restraints: 7646 sinusoidal: 4329 harmonic: 3317 Sorted by residual: dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N SER A 87 " pdb=" CA SER A 87 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR A1201 " pdb=" C TYR A1201 " pdb=" N SER A1202 " pdb=" CA SER A1202 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" N ASP A 182 " pdb=" CA ASP A 182 " ideal model delta harmonic sigma weight residual 180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 7643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1261 0.031 - 0.063: 445 0.063 - 0.094: 174 0.094 - 0.125: 84 0.125 - 0.157: 71 Chirality restraints: 2035 Sorted by residual: chirality pdb=" C1' A D 42 " pdb=" O4' A D 42 " pdb=" C2' A D 42 " pdb=" N9 A D 42 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" C2' C D 18 " pdb=" C3' C D 18 " pdb=" O2' C D 18 " pdb=" C1' C D 18 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C2' U D 59 " pdb=" C3' U D 59 " pdb=" O2' U D 59 " pdb=" C1' U D 59 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2032 not shown) Planarity restraints: 1751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 42 " -0.022 2.00e-02 2.50e+03 1.01e-02 2.81e+00 pdb=" N9 A D 42 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A D 42 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A D 42 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D 42 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A D 42 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A D 42 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 42 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A D 42 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 42 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 54 " 0.020 2.00e-02 2.50e+03 8.80e-03 2.32e+00 pdb=" N9 G D 54 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G D 54 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G D 54 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G D 54 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G D 54 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G D 54 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G D 54 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G D 54 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G D 54 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G D 54 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G D 54 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 49 " 0.019 2.00e-02 2.50e+03 8.88e-03 2.17e+00 pdb=" N9 A D 49 " -0.020 2.00e-02 2.50e+03 pdb=" C8 A D 49 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A D 49 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A D 49 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A D 49 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A D 49 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A D 49 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A D 49 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 49 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A D 49 " -0.002 2.00e-02 2.50e+03 ... (remaining 1748 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 4 2.02 - 2.74: 1168 2.74 - 3.46: 17088 3.46 - 4.18: 30430 4.18 - 4.90: 48617 Nonbonded interactions: 97307 Sorted by model distance: nonbonded pdb=" NZ LYS A 510 " pdb=" O5' A D 5 " model vdw 1.298 3.120 nonbonded pdb=" ND2 ASN A 77 " pdb=" O2 U D 59 " model vdw 1.299 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" C5 C D 18 " model vdw 1.433 3.420 nonbonded pdb=" SD MET A 495 " pdb=" C1' DA B 24 " model vdw 1.771 3.830 nonbonded pdb=" OG SER A 719 " pdb=" OE1 GLU A 722 " model vdw 2.132 3.040 ... (remaining 97302 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 group one per residue 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: 0.490 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.250 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.004 0.057 12619 Z= 0.328 Angle : 0.705 6.978 17640 Z= 0.536 Chirality : 0.047 0.157 2035 Planarity : 0.004 0.034 1751 Dihedral : 16.621 86.247 5498 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.77 (0.25), residues: 1123 helix: 1.10 (0.22), residues: 561 sheet: 0.64 (0.54), residues: 83 loop : -0.10 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 69 TYR 0.016 0.001 TYR A1141 PHE 0.018 0.002 PHE A 164 TRP 0.020 0.002 TRP A1126 HIS 0.005 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.33 (12619) covalent geometry : angle 0.70514 / 0.54 (17640) hydrogen bonds : bond 0.16616 / 11.38 ( 572) hydrogen bonds : angle 5.71791 / 3.95 ( 1541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.5602 (mtt) cc_final: 0.5283 (ttm) REVERT: A 621 LEU cc_start: 0.9561 (tp) cc_final: 0.9337 (tp) REVERT: A 648 MET cc_start: 0.9387 (mmm) cc_final: 0.8930 (mmm) REVERT: A 930 HIS cc_start: 0.8104 (m-70) cc_final: 0.7868 (m-70) REVERT: A 1172 SER cc_start: 0.9493 (m) cc_final: 0.8924 (p) REVERT: A 1238 LEU cc_start: 0.9563 (mt) cc_final: 0.9291 (pp) REVERT: A 1357 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7872 (mp0) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1221 time to fit residues: 34.8246 Evaluate side-chains 108 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 224 ASN A 265 GLN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 HIS A1261 GLN A1286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.054509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.037417 restraints weight = 78925.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038962 restraints weight = 40372.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.040007 restraints weight = 26749.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.040606 restraints weight = 20548.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.041105 restraints weight = 17475.593| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12619 Z= 0.197 Angle : 0.689 11.415 17640 Z= 0.380 Chirality : 0.044 0.247 2035 Planarity : 0.005 0.056 1751 Dihedral : 18.959 82.933 3122 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.71 % Rotamer: Outliers : 1.78 % Allowed : 8.52 % Favored : 89.69 % 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: 1123 helix: 0.84 (0.22), residues: 567 sheet: 0.69 (0.56), residues: 92 loop : -0.18 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 71 TYR 0.018 0.002 TYR A1141 PHE 0.017 0.002 PHE A 351 TRP 0.010 0.001 TRP A 659 HIS 0.007 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (12619) covalent geometry : angle 0.68936 / 0.38 (17640) hydrogen bonds : bond 0.05865 / 3.97 ( 572) hydrogen bonds : angle 4.99208 / 3.45 ( 1541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9671 (mtmt) cc_final: 0.9280 (ttpt) REVERT: A 321 MET cc_start: 0.9490 (mmp) cc_final: 0.9243 (mmm) REVERT: A 492 ILE cc_start: 0.9841 (mm) cc_final: 0.9597 (tt) REVERT: A 510 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9329 (ptmm) REVERT: A 534 MET cc_start: 0.6722 (mtt) cc_final: 0.6043 (ttm) REVERT: A 564 LEU cc_start: 0.9622 (tt) cc_final: 0.9358 (pp) REVERT: A 623 LEU cc_start: 0.9630 (tt) cc_final: 0.9415 (tt) REVERT: A 648 MET cc_start: 0.9715 (mmm) cc_final: 0.9079 (mmm) REVERT: A 652 LYS cc_start: 0.9444 (mttt) cc_final: 0.8848 (mmmm) REVERT: A 751 MET cc_start: 0.9371 (tpp) cc_final: 0.9137 (ttt) REVERT: A 1324 PHE cc_start: 0.8633 (p90) cc_final: 0.8087 (p90) REVERT: A 1357 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8506 (mp0) outliers start: 18 outliers final: 9 residues processed: 120 average time/residue: 0.0995 time to fit residues: 17.7186 Evaluate side-chains 105 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1259 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 91 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 40.0000 chunk 94 optimal weight: 2.9990 chunk 119 optimal weight: 40.0000 chunk 71 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN A1101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.053272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.036348 restraints weight = 83701.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037921 restraints weight = 42256.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038941 restraints weight = 27889.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.039595 restraints weight = 21528.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.039947 restraints weight = 18299.538| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12619 Z= 0.268 Angle : 0.701 10.672 17640 Z= 0.385 Chirality : 0.043 0.223 2035 Planarity : 0.005 0.065 1751 Dihedral : 19.026 83.195 3122 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.92 % Favored : 95.99 % Rotamer: Outliers : 2.18 % Allowed : 8.92 % Favored : 88.90 % 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: 0.34 (0.24), residues: 1123 helix: 0.64 (0.21), residues: 563 sheet: 1.13 (0.58), residues: 81 loop : -0.32 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 400 TYR 0.018 0.002 TYR A 973 PHE 0.015 0.002 PHE A 491 TRP 0.014 0.002 TRP A 659 HIS 0.009 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.27 (12619) covalent geometry : angle 0.70130 / 0.39 (17640) hydrogen bonds : bond 0.05854 / 3.99 ( 572) hydrogen bonds : angle 5.05683 / 3.49 ( 1541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9694 (mtmt) cc_final: 0.9173 (ttpt) REVERT: A 442 LYS cc_start: 0.9731 (tttt) cc_final: 0.9414 (ttpp) REVERT: A 495 MET cc_start: 0.9560 (mpp) cc_final: 0.9119 (mpp) REVERT: A 534 MET cc_start: 0.6885 (mtt) cc_final: 0.5909 (ttm) REVERT: A 648 MET cc_start: 0.9689 (mmm) cc_final: 0.9150 (mmm) REVERT: A 751 MET cc_start: 0.9366 (tpp) cc_final: 0.9144 (ttt) REVERT: A 1169 MET cc_start: 0.9151 (ttp) cc_final: 0.7873 (tmm) REVERT: A 1219 GLU cc_start: 0.9121 (tp30) cc_final: 0.8704 (tp30) REVERT: A 1221 GLN cc_start: 0.9326 (mt0) cc_final: 0.9099 (mm-40) REVERT: A 1313 PHE cc_start: 0.9483 (m-80) cc_final: 0.9280 (m-10) REVERT: A 1357 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8299 (mp0) outliers start: 22 outliers final: 14 residues processed: 100 average time/residue: 0.0888 time to fit residues: 13.4071 Evaluate side-chains 97 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.3980 chunk 14 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 121 optimal weight: 30.0000 chunk 46 optimal weight: 4.9990 chunk 112 optimal weight: 50.0000 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037303 restraints weight = 81154.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.038895 restraints weight = 41094.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.039955 restraints weight = 27126.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.040553 restraints weight = 20891.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.041028 restraints weight = 17863.892| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12619 Z= 0.139 Angle : 0.601 10.729 17640 Z= 0.331 Chirality : 0.041 0.410 2035 Planarity : 0.004 0.060 1751 Dihedral : 18.989 84.306 3122 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.71 % Rotamer: Outliers : 1.98 % Allowed : 9.12 % Favored : 88.90 % 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: 0.58 (0.25), residues: 1123 helix: 0.90 (0.21), residues: 564 sheet: 1.04 (0.58), residues: 81 loop : -0.25 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.012 0.001 TYR A 973 PHE 0.015 0.001 PHE A1204 TRP 0.010 0.001 TRP A 659 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (12619) covalent geometry : angle 0.60140 / 0.33 (17640) hydrogen bonds : bond 0.04609 / 3.09 ( 572) hydrogen bonds : angle 4.68759 / 3.23 ( 1541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9675 (mtmt) cc_final: 0.9117 (ttpt) REVERT: A 101 LEU cc_start: 0.9460 (tt) cc_final: 0.8946 (mm) REVERT: A 398 LEU cc_start: 0.9303 (mt) cc_final: 0.8812 (mt) REVERT: A 441 GLU cc_start: 0.9542 (pt0) cc_final: 0.8971 (pp20) REVERT: A 442 LYS cc_start: 0.9698 (tttt) cc_final: 0.9256 (mmmm) REVERT: A 492 ILE cc_start: 0.9803 (mm) cc_final: 0.9556 (tt) REVERT: A 534 MET cc_start: 0.6930 (mtt) cc_final: 0.5921 (ttm) REVERT: A 564 LEU cc_start: 0.9602 (tt) cc_final: 0.9347 (pp) REVERT: A 631 MET cc_start: 0.9692 (OUTLIER) cc_final: 0.9392 (pmm) REVERT: A 648 MET cc_start: 0.9713 (mmm) cc_final: 0.9155 (mmm) REVERT: A 751 MET cc_start: 0.9336 (tpp) cc_final: 0.8966 (ttt) REVERT: A 1219 GLU cc_start: 0.9148 (tp30) cc_final: 0.8405 (tp30) REVERT: A 1357 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8223 (mp0) outliers start: 20 outliers final: 11 residues processed: 103 average time/residue: 0.0926 time to fit residues: 14.6251 Evaluate side-chains 99 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 109 optimal weight: 30.0000 chunk 108 optimal weight: 0.9990 chunk 4 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 122 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 30.0000 chunk 76 optimal weight: 40.0000 chunk 44 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.052524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.035740 restraints weight = 84339.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.037222 restraints weight = 42857.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.038243 restraints weight = 28422.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038892 restraints weight = 21897.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039238 restraints weight = 18613.459| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12619 Z= 0.218 Angle : 0.628 9.289 17640 Z= 0.348 Chirality : 0.040 0.205 2035 Planarity : 0.004 0.061 1751 Dihedral : 19.026 85.418 3122 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 2.18 % Allowed : 11.10 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.24), residues: 1123 helix: 0.81 (0.21), residues: 569 sheet: 0.95 (0.59), residues: 81 loop : -0.34 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 967 TYR 0.014 0.002 TYR A 973 PHE 0.018 0.002 PHE A 966 TRP 0.015 0.002 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.22 (12619) covalent geometry : angle 0.62779 / 0.35 (17640) hydrogen bonds : bond 0.05217 / 3.52 ( 572) hydrogen bonds : angle 4.84872 / 3.33 ( 1541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9697 (mtmt) cc_final: 0.9207 (ttpt) REVERT: A 442 LYS cc_start: 0.9749 (tttt) cc_final: 0.9453 (ttpp) REVERT: A 492 ILE cc_start: 0.9817 (mm) cc_final: 0.9598 (tt) REVERT: A 495 MET cc_start: 0.9541 (mpp) cc_final: 0.9166 (mpp) REVERT: A 510 LYS cc_start: 0.9652 (ptmm) cc_final: 0.9397 (ptmt) REVERT: A 516 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8936 (mt-10) REVERT: A 534 MET cc_start: 0.7061 (mtt) cc_final: 0.6038 (ttm) REVERT: A 648 MET cc_start: 0.9688 (mmm) cc_final: 0.9077 (mmm) REVERT: A 1089 MET cc_start: 0.8843 (mmt) cc_final: 0.8615 (mmp) REVERT: A 1219 GLU cc_start: 0.9116 (tp30) cc_final: 0.8842 (tp30) REVERT: A 1357 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8677 (tp30) outliers start: 22 outliers final: 15 residues processed: 89 average time/residue: 0.0872 time to fit residues: 11.9724 Evaluate side-chains 94 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 95 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 124 optimal weight: 50.0000 chunk 80 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.050721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.034332 restraints weight = 85821.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035788 restraints weight = 44099.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.036667 restraints weight = 29368.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037376 restraints weight = 22921.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.037793 restraints weight = 19321.742| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12619 Z= 0.252 Angle : 0.660 11.691 17640 Z= 0.366 Chirality : 0.041 0.218 2035 Planarity : 0.004 0.062 1751 Dihedral : 19.139 86.371 3122 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 1.68 % Allowed : 12.19 % Favored : 86.12 % 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: 0.19 (0.24), residues: 1123 helix: 0.65 (0.21), residues: 568 sheet: 0.76 (0.60), residues: 81 loop : -0.53 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 557 TYR 0.013 0.002 TYR A 132 PHE 0.015 0.002 PHE A 352 TRP 0.017 0.002 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.25 (12619) covalent geometry : angle 0.66030 / 0.37 (17640) hydrogen bonds : bond 0.05270 / 3.52 ( 572) hydrogen bonds : angle 4.91782 / 3.37 ( 1541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9684 (mtmt) cc_final: 0.9236 (ttpt) REVERT: A 101 LEU cc_start: 0.9542 (tt) cc_final: 0.9206 (pp) REVERT: A 442 LYS cc_start: 0.9765 (tttt) cc_final: 0.9555 (mmmm) REVERT: A 510 LYS cc_start: 0.9672 (ptmm) cc_final: 0.9414 (ptmt) REVERT: A 534 MET cc_start: 0.7003 (mtt) cc_final: 0.6001 (ttm) REVERT: A 564 LEU cc_start: 0.9638 (tt) cc_final: 0.9391 (pp) REVERT: A 648 MET cc_start: 0.9675 (mmm) cc_final: 0.9112 (mmm) REVERT: A 751 MET cc_start: 0.9427 (tpp) cc_final: 0.9213 (ttm) REVERT: A 763 MET cc_start: 0.2290 (ttt) cc_final: 0.1902 (ttp) REVERT: A 1089 MET cc_start: 0.8808 (mmt) cc_final: 0.8539 (mpp) REVERT: A 1166 ILE cc_start: 0.9551 (mm) cc_final: 0.9290 (pt) REVERT: A 1169 MET cc_start: 0.9303 (ttp) cc_final: 0.7962 (tmm) REVERT: A 1219 GLU cc_start: 0.9267 (tp30) cc_final: 0.8894 (tp30) REVERT: A 1350 GLN cc_start: 0.9164 (mp10) cc_final: 0.8957 (mp10) REVERT: A 1357 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8636 (tp30) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 0.0847 time to fit residues: 11.4318 Evaluate side-chains 90 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 123 optimal weight: 50.0000 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.034496 restraints weight = 85346.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035946 restraints weight = 43619.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.036909 restraints weight = 28832.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.037549 restraints weight = 22286.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037904 restraints weight = 18866.211| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12619 Z= 0.191 Angle : 0.613 14.327 17640 Z= 0.336 Chirality : 0.040 0.209 2035 Planarity : 0.004 0.060 1751 Dihedral : 19.122 87.174 3122 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 1.29 % Allowed : 12.98 % Favored : 85.73 % 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: 0.37 (0.24), residues: 1123 helix: 0.83 (0.21), residues: 570 sheet: 0.74 (0.61), residues: 83 loop : -0.46 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 557 TYR 0.011 0.001 TYR A 5 PHE 0.014 0.002 PHE A 518 TRP 0.011 0.001 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 (12619) covalent geometry : angle 0.61261 / 0.34 (17640) hydrogen bonds : bond 0.04699 / 3.12 ( 572) hydrogen bonds : angle 4.75171 / 3.26 ( 1541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9662 (mtmt) cc_final: 0.9207 (ttpt) REVERT: A 101 LEU cc_start: 0.9559 (tt) cc_final: 0.9230 (pp) REVERT: A 442 LYS cc_start: 0.9743 (tttt) cc_final: 0.9502 (mmmm) REVERT: A 495 MET cc_start: 0.9579 (mpp) cc_final: 0.9196 (mpp) REVERT: A 510 LYS cc_start: 0.9662 (ptmm) cc_final: 0.9410 (ptmt) REVERT: A 534 MET cc_start: 0.7033 (mtt) cc_final: 0.6030 (ttm) REVERT: A 564 LEU cc_start: 0.9619 (tt) cc_final: 0.9372 (pp) REVERT: A 648 MET cc_start: 0.9664 (mmm) cc_final: 0.9046 (mmm) REVERT: A 763 MET cc_start: 0.1947 (ttt) cc_final: 0.1692 (ttp) REVERT: A 1089 MET cc_start: 0.8789 (mmt) cc_final: 0.8483 (mpp) REVERT: A 1166 ILE cc_start: 0.9554 (mm) cc_final: 0.9292 (pt) REVERT: A 1169 MET cc_start: 0.9298 (ttp) cc_final: 0.7988 (tmm) REVERT: A 1219 GLU cc_start: 0.9227 (tp30) cc_final: 0.8774 (tp30) REVERT: A 1357 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8544 (tp30) outliers start: 13 outliers final: 11 residues processed: 88 average time/residue: 0.0870 time to fit residues: 11.6443 Evaluate side-chains 86 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 76 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.051155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.034774 restraints weight = 85105.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036202 restraints weight = 43155.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.037210 restraints weight = 28621.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037766 restraints weight = 22001.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038243 restraints weight = 18841.361| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12619 Z= 0.160 Angle : 0.594 11.907 17640 Z= 0.324 Chirality : 0.039 0.201 2035 Planarity : 0.004 0.057 1751 Dihedral : 19.094 87.679 3122 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 0.99 % Allowed : 14.17 % Favored : 84.84 % 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: 0.48 (0.25), residues: 1123 helix: 0.98 (0.21), residues: 570 sheet: 0.20 (0.62), residues: 79 loop : -0.38 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1212 TYR 0.008 0.001 TYR A 430 PHE 0.012 0.001 PHE A 518 TRP 0.009 0.001 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (12619) covalent geometry : angle 0.59443 / 0.32 (17640) hydrogen bonds : bond 0.04445 / 2.94 ( 572) hydrogen bonds : angle 4.63024 / 3.18 ( 1541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9662 (mtmt) cc_final: 0.9196 (ttpt) REVERT: A 332 LEU cc_start: 0.9396 (tp) cc_final: 0.8667 (pp) REVERT: A 442 LYS cc_start: 0.9730 (tttt) cc_final: 0.9491 (mmmm) REVERT: A 495 MET cc_start: 0.9600 (mpp) cc_final: 0.9254 (mpp) REVERT: A 510 LYS cc_start: 0.9657 (ptmm) cc_final: 0.9423 (ptmt) REVERT: A 534 MET cc_start: 0.7117 (mtt) cc_final: 0.6111 (ttm) REVERT: A 564 LEU cc_start: 0.9609 (tt) cc_final: 0.9376 (pp) REVERT: A 648 MET cc_start: 0.9677 (mmm) cc_final: 0.9061 (mmm) REVERT: A 751 MET cc_start: 0.9213 (ttm) cc_final: 0.8985 (ppp) REVERT: A 763 MET cc_start: 0.1879 (ttt) cc_final: 0.1600 (ttp) REVERT: A 1089 MET cc_start: 0.8758 (mmt) cc_final: 0.8007 (mmt) REVERT: A 1166 ILE cc_start: 0.9547 (mm) cc_final: 0.9237 (pt) REVERT: A 1219 GLU cc_start: 0.9243 (tp30) cc_final: 0.8661 (tp30) REVERT: A 1350 GLN cc_start: 0.9109 (mp10) cc_final: 0.8878 (mp10) REVERT: A 1357 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8540 (tp30) outliers start: 10 outliers final: 10 residues processed: 84 average time/residue: 0.0854 time to fit residues: 11.1416 Evaluate side-chains 88 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 85 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 116 optimal weight: 40.0000 chunk 80 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.050164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.033942 restraints weight = 87091.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.035393 restraints weight = 44455.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.036357 restraints weight = 29457.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.036916 restraints weight = 22738.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.037374 restraints weight = 19436.705| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12619 Z= 0.230 Angle : 0.648 13.534 17640 Z= 0.352 Chirality : 0.040 0.289 2035 Planarity : 0.004 0.058 1751 Dihedral : 19.108 88.064 3122 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 1.19 % Allowed : 13.88 % Favored : 84.94 % 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: 0.28 (0.24), residues: 1123 helix: 0.81 (0.21), residues: 573 sheet: 0.06 (0.61), residues: 79 loop : -0.47 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 557 TYR 0.010 0.001 TYR A 430 PHE 0.014 0.002 PHE A 491 TRP 0.014 0.002 TRP A 659 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.23 (12619) covalent geometry : angle 0.64795 / 0.35 (17640) hydrogen bonds : bond 0.05119 / 3.40 ( 572) hydrogen bonds : angle 4.78894 / 3.28 ( 1541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9669 (mtmt) cc_final: 0.9220 (ttpt) REVERT: A 442 LYS cc_start: 0.9744 (tttt) cc_final: 0.9467 (mmmm) REVERT: A 510 LYS cc_start: 0.9678 (ptmm) cc_final: 0.9414 (ptmt) REVERT: A 534 MET cc_start: 0.7226 (mtt) cc_final: 0.6111 (ttm) REVERT: A 564 LEU cc_start: 0.9639 (tt) cc_final: 0.9408 (pp) REVERT: A 648 MET cc_start: 0.9673 (mmm) cc_final: 0.9127 (mmm) REVERT: A 763 MET cc_start: 0.1971 (ttt) cc_final: 0.1674 (ttp) REVERT: A 939 MET cc_start: 0.8802 (mmt) cc_final: 0.7398 (ttt) REVERT: A 1089 MET cc_start: 0.8785 (mmt) cc_final: 0.8037 (mmt) REVERT: A 1166 ILE cc_start: 0.9564 (mm) cc_final: 0.9318 (pt) REVERT: A 1169 MET cc_start: 0.9326 (ttp) cc_final: 0.7949 (tmm) REVERT: A 1213 MET cc_start: 0.8750 (tpt) cc_final: 0.8476 (tpp) REVERT: A 1326 TYR cc_start: 0.9104 (t80) cc_final: 0.8143 (t80) REVERT: A 1350 GLN cc_start: 0.9114 (mp10) cc_final: 0.8865 (mp10) REVERT: A 1357 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8522 (tp30) outliers start: 12 outliers final: 12 residues processed: 84 average time/residue: 0.0881 time to fit residues: 11.3918 Evaluate side-chains 88 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 42 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.051008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.034625 restraints weight = 85262.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036117 restraints weight = 42911.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.037123 restraints weight = 28324.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.037688 restraints weight = 21774.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038148 restraints weight = 18592.272| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12619 Z= 0.147 Angle : 0.603 14.038 17640 Z= 0.323 Chirality : 0.039 0.348 2035 Planarity : 0.004 0.056 1751 Dihedral : 19.062 88.471 3122 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.92 % Favored : 95.99 % Rotamer: Outliers : 1.29 % Allowed : 13.78 % Favored : 84.94 % 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: 0.51 (0.25), residues: 1123 helix: 1.02 (0.21), residues: 571 sheet: 0.15 (0.61), residues: 79 loop : -0.38 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.007 0.001 TYR A 347 PHE 0.013 0.001 PHE A 518 TRP 0.009 0.001 TRP A 659 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (12619) covalent geometry : angle 0.60289 / 0.32 (17640) hydrogen bonds : bond 0.04323 / 2.85 ( 572) hydrogen bonds : angle 4.59336 / 3.15 ( 1541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9651 (mtmt) cc_final: 0.9174 (ttpt) REVERT: A 321 MET cc_start: 0.9315 (mmp) cc_final: 0.8935 (mmm) REVERT: A 332 LEU cc_start: 0.9389 (tp) cc_final: 0.8663 (pp) REVERT: A 442 LYS cc_start: 0.9729 (tttt) cc_final: 0.9444 (mmmm) REVERT: A 495 MET cc_start: 0.9624 (mpp) cc_final: 0.9280 (mpp) REVERT: A 510 LYS cc_start: 0.9663 (ptmm) cc_final: 0.9364 (ptmm) REVERT: A 534 MET cc_start: 0.7286 (mtt) cc_final: 0.6193 (ttm) REVERT: A 564 LEU cc_start: 0.9612 (tt) cc_final: 0.9381 (pp) REVERT: A 648 MET cc_start: 0.9687 (mmm) cc_final: 0.9086 (mmm) REVERT: A 763 MET cc_start: 0.1835 (ttt) cc_final: 0.1562 (ttp) REVERT: A 939 MET cc_start: 0.8759 (mmt) cc_final: 0.7351 (ttt) REVERT: A 1089 MET cc_start: 0.8777 (mmt) cc_final: 0.8338 (mmt) REVERT: A 1166 ILE cc_start: 0.9540 (mm) cc_final: 0.9273 (mt) REVERT: A 1169 MET cc_start: 0.9359 (ttp) cc_final: 0.8127 (tmm) REVERT: A 1213 MET cc_start: 0.8838 (tpt) cc_final: 0.8500 (tpp) REVERT: A 1350 GLN cc_start: 0.9126 (mp10) cc_final: 0.8885 (mp10) REVERT: A 1357 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8508 (tp30) outliers start: 13 outliers final: 13 residues processed: 86 average time/residue: 0.0918 time to fit residues: 12.1120 Evaluate side-chains 90 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 121 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.049944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.033802 restraints weight = 87358.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.035262 restraints weight = 44360.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036229 restraints weight = 29257.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.036764 restraints weight = 22518.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.037219 restraints weight = 19312.385| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12619 Z= 0.234 Angle : 0.642 12.146 17640 Z= 0.350 Chirality : 0.040 0.291 2035 Planarity : 0.004 0.057 1751 Dihedral : 19.087 88.767 3122 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 1.49 % Allowed : 13.78 % Favored : 84.74 % 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: 0.33 (0.24), residues: 1123 helix: 0.86 (0.21), residues: 567 sheet: 0.09 (0.62), residues: 79 loop : -0.42 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 753 TYR 0.010 0.001 TYR A 430 PHE 0.013 0.002 PHE A 970 TRP 0.013 0.002 TRP A 659 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.23 (12619) covalent geometry : angle 0.64174 / 0.35 (17640) hydrogen bonds : bond 0.05052 / 3.34 ( 572) hydrogen bonds : angle 4.77832 / 3.28 ( 1541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.59 seconds wall clock time: 34 minutes 41.41 seconds (2081.41 seconds total)