Starting phenix.real_space_refine on Thu Aug 6 02:16:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmh_37652/08_2026/8wmh_37652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmh_37652/08_2026/8wmh_37652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wmh_37652/08_2026/8wmh_37652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmh_37652/08_2026/8wmh_37652.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmh_37652/08_2026/8wmh_37652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmh_37652/08_2026/8wmh_37652.cif" } resolution = 2.6 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= 0.001 sd= 0.016 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 141 5.49 5 S 19 5.16 5 C 7736 2.51 5 N 2256 2.21 5 O 2790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 12942 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1198, 9972 Classifications: {'peptide': 1198} Link IDs: {'PTRANS': 30, 'TRANS': 1167} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1198, 9972 Classifications: {'peptide': 1198} Link IDs: {'PTRANS': 30, 'TRANS': 1167} Chain breaks: 2 bond proxies already assigned to first conformer: 10172 Chain: "O" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1900 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 46, 'rna3p_pyr': 36} Link IDs: {'rna2p': 6, 'rna3p': 82} Chain breaks: 1 Chain: "C" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "E" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP A 672 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP A 672 " occ=0.55 Time building chain proxies: 4.50, per 1000 atoms: 0.35 Number of scatterers: 12942 At special positions: 0 Unit cell: (98.5075, 115.828, 137.477, 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 141 15.00 O 2790 8.00 N 2256 7.00 C 7736 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: 1.08 Conformation dependent library (CDL) restraints added in 815.1 milliseconds 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 44.5% alpha, 11.6% beta 54 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.572A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 88 Processing helix chain 'A' and resid 92 through 98 removed outlier: 3.764A pdb=" N GLN A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 removed outlier: 3.518A pdb=" N PHE A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.737A pdb=" N HIS A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 291 through 303 Processing helix chain 'A' and resid 317 through 334 removed outlier: 4.039A pdb=" N TYR A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 6.117A pdb=" N GLU A 338 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 452 through 465 removed outlier: 3.542A pdb=" N PHE A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.638A pdb=" N THR A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 576 through 588 Proline residue: A 585 - end of helix Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.718A pdb=" N TYR A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.589A pdb=" N ARG A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.882A pdb=" N LEU A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 removed outlier: 3.625A pdb=" N GLU A 684 " --> pdb=" O ASN A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 935 removed outlier: 3.623A pdb=" N ILE A 934 " --> pdb=" O THR A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 943 Processing helix chain 'A' and resid 965 through 976 removed outlier: 3.634A pdb=" N THR A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 997 Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1025 through 1030 removed outlier: 4.105A pdb=" N ILE A1029 " --> pdb=" O LYS A1026 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASP A1030 " --> pdb=" O LYS A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1044 removed outlier: 4.373A pdb=" N ALA A1035 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A1044 " --> pdb=" O VAL A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1054 Processing helix chain 'A' and resid 1063 through 1070 Processing helix chain 'A' and resid 1101 through 1112 Processing helix chain 'A' and resid 1193 through 1198 Processing helix chain 'A' and resid 1203 through 1216 Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1225 through 1235 Processing helix chain 'A' and resid 1265 through 1270 removed outlier: 4.079A pdb=" N LYS A1269 " --> pdb=" O GLY A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1309 Processing helix chain 'A' and resid 1353 through 1358 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715 removed outlier: 6.589A pdb=" N ASN A 4 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS A 713 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 6 " --> pdb=" O HIS A 713 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU A 715 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU A 8 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 3 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 15 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A 36 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP A 17 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N MET A 34 " --> pdb=" O TRP A 17 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU A 19 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.904A pdb=" N LYS A 107 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 204 removed outlier: 3.538A pdb=" N LYS A 247 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 248 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 215 removed outlier: 4.257A pdb=" N GLU A 214 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 400 removed outlier: 4.984A pdb=" N LEU A 412 " --> pdb=" O CYS A 393 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N LEU A 395 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N GLN A 410 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N PHE A 397 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N HIS A 408 " --> pdb=" O PHE A 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 469 removed outlier: 3.678A pdb=" N VAL A 469 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 495 " --> pdb=" O VAL A 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 4.314A pdb=" N GLN A1094 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1124 through 1126 Processing sheet with id=AB2, first strand: chain 'A' and resid 1130 through 1137 Processing sheet with id=AB3, first strand: chain 'A' and resid 1166 through 1168 removed outlier: 4.124A pdb=" N LEU A1181 " --> pdb=" O VAL A1168 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1260 through 1261 Processing sheet with id=AB5, first strand: chain 'A' and resid 1293 through 1298 removed outlier: 4.661A pdb=" N PHE A1282 " --> pdb=" O ILE A1298 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N PHE A1283 " --> pdb=" O ASP A1327 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP A1327 " --> pdb=" O PHE A1283 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A1285 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1370 through 1375 removed outlier: 6.897A pdb=" N GLU A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR A1366 " --> pdb=" O GLU A1370 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR A1372 " --> pdb=" O GLU A1364 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 130 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 1.38 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: 2803 1.33 - 1.45: 3643 1.45 - 1.57: 6748 1.57 - 1.69: 278 1.69 - 1.81: 31 Bond restraints: 13503 Sorted by residual: bond pdb=" C3' DC C 43 " pdb=" C2' DC C 43 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.52e+00 bond pdb=" N GLU A1393 " pdb=" CA GLU A1393 " ideal model delta sigma weight residual 1.459 1.427 0.033 1.20e-02 6.94e+03 7.34e+00 bond pdb=" CA ARG A1122 " pdb=" C ARG A1122 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.35e-02 5.49e+03 6.71e+00 bond pdb=" C5' DG E 8 " pdb=" C4' DG E 8 " ideal model delta sigma weight residual 1.512 1.527 -0.015 7.00e-03 2.04e+04 4.85e+00 bond pdb=" C3' DC E 14 " pdb=" C2' DC E 14 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.69e+00 ... (remaining 13498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 18052 1.41 - 2.82: 682 2.82 - 4.23: 85 4.23 - 5.64: 18 5.64 - 7.06: 3 Bond angle restraints: 18840 Sorted by residual: angle pdb=" N ARG A 692 " pdb=" CA ARG A 692 " pdb=" C ARG A 692 " ideal model delta sigma weight residual 111.14 106.19 4.95 1.08e+00 8.57e-01 2.10e+01 angle pdb=" O4' DA C 52 " pdb=" C4' DA C 52 " pdb=" C3' DA C 52 " ideal model delta sigma weight residual 106.00 103.71 2.29 6.00e-01 2.78e+00 1.46e+01 angle pdb=" C3' G O 107 " pdb=" O3' G O 107 " pdb=" P C O 108 " ideal model delta sigma weight residual 119.70 124.06 -4.36 1.20e+00 6.94e-01 1.32e+01 angle pdb=" O5' A O 84 " pdb=" C5' A O 84 " pdb=" C4' A O 84 " ideal model delta sigma weight residual 109.40 112.29 -2.89 8.00e-01 1.56e+00 1.30e+01 angle pdb=" O5' A O 27 " pdb=" C5' A O 27 " pdb=" C4' A O 27 " ideal model delta sigma weight residual 109.40 112.26 -2.86 8.00e-01 1.56e+00 1.27e+01 ... (remaining 18835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 7223 24.90 - 49.81: 624 49.81 - 74.71: 248 74.71 - 99.62: 19 99.62 - 124.52: 3 Dihedral angle restraints: 8117 sinusoidal: 4590 harmonic: 3527 Sorted by residual: dihedral pdb=" O4' C O 113 " pdb=" C1' C O 113 " pdb=" N1 C O 113 " pdb=" C2 C O 113 " ideal model delta sinusoidal sigma weight residual -160.00 -114.43 -45.57 1 1.50e+01 4.44e-03 1.28e+01 dihedral pdb=" C4' DA E 17 " pdb=" C3' DA E 17 " pdb=" O3' DA E 17 " pdb=" P DT E 18 " ideal model delta sinusoidal sigma weight residual 220.00 95.48 124.52 1 3.50e+01 8.16e-04 1.23e+01 dihedral pdb=" O4' G O 94 " pdb=" C1' G O 94 " pdb=" N9 G O 94 " pdb=" C4 G O 94 " ideal model delta sinusoidal sigma weight residual -106.00 -156.14 50.14 1 1.70e+01 3.46e-03 1.19e+01 ... (remaining 8114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1518 0.041 - 0.081: 382 0.081 - 0.122: 120 0.122 - 0.163: 91 0.163 - 0.204: 3 Chirality restraints: 2114 Sorted by residual: chirality pdb=" C3' DA E 17 " pdb=" C4' DA E 17 " pdb=" O3' DA E 17 " pdb=" C2' DA E 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLU A 72 " pdb=" N GLU A 72 " pdb=" C GLU A 72 " pdb=" CB GLU A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" C3' G O 107 " pdb=" C4' G O 107 " pdb=" O3' G O 107 " pdb=" C2' G O 107 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 2111 not shown) Planarity restraints: 1895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 68 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C ARG A 68 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG A 68 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 69 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 122 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" CG ASP A 122 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 122 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 122 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 419 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 420 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 420 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 420 " 0.023 5.00e-02 4.00e+02 ... (remaining 1892 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1058 2.74 - 3.28: 12693 3.28 - 3.82: 23035 3.82 - 4.36: 27866 4.36 - 4.90: 43888 Nonbonded interactions: 108540 Sorted by model distance: nonbonded pdb=" O2' A O 114 " pdb=" O4' A O 115 " model vdw 2.196 3.040 nonbonded pdb=" O LYS A 109 " pdb=" OG1 THR A 112 " model vdw 2.221 3.040 nonbonded pdb=" OG SER A 385 " pdb=" OP1 C O 118 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLU A1132 " pdb=" O2' U O 86 " model vdw 2.235 3.040 nonbonded pdb=" O2' G O 107 " pdb=" OP1 C O 108 " model vdw 2.247 3.040 ... (remaining 108535 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.640 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:7.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 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 : 0.003 0.035 13503 Z= 0.239 Angle : 0.609 7.056 18840 Z= 0.424 Chirality : 0.048 0.204 2114 Planarity : 0.003 0.041 1895 Dihedral : 19.417 124.521 5835 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.36 % Allowed : 0.82 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1195 helix: 0.98 (0.24), residues: 462 sheet: -0.59 (0.45), residues: 131 loop : -0.61 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1028 TYR 0.012 0.001 TYR A1380 PHE 0.017 0.001 PHE A 990 TRP 0.024 0.001 TRP A 528 HIS 0.003 0.001 HIS A1033 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.24 (13503) covalent geometry : angle 0.60868 / 0.42 (18840) hydrogen bonds : bond 0.15083 / 10.45 ( 516) hydrogen bonds : angle 5.84872 / 4.04 ( 1325) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7347 (tp30) cc_final: 0.6853 (tp30) REVERT: A 63 LYS cc_start: 0.7101 (tptm) cc_final: 0.6580 (tptm) REVERT: A 64 TYR cc_start: 0.7694 (m-80) cc_final: 0.7444 (m-80) REVERT: A 79 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 103 LYS cc_start: 0.7643 (tptm) cc_final: 0.7363 (tptm) REVERT: A 129 PHE cc_start: 0.7655 (m-80) cc_final: 0.7208 (m-80) REVERT: A 265 PHE cc_start: 0.2996 (m-80) cc_final: 0.2680 (m-80) REVERT: A 280 LYS cc_start: 0.7240 (ttpt) cc_final: 0.6965 (ttmt) REVERT: A 317 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6240 (mm-30) REVERT: A 357 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6766 (mm-30) REVERT: A 373 MET cc_start: 0.8028 (ttp) cc_final: 0.7767 (ttp) REVERT: A 381 ARG cc_start: 0.7245 (mtt90) cc_final: 0.6955 (mpt180) REVERT: A 656 MET cc_start: -0.1031 (pmm) cc_final: -0.1284 (pmm) REVERT: A 980 ASP cc_start: 0.6436 (t0) cc_final: 0.6123 (t0) REVERT: A 1124 ILE cc_start: 0.7378 (pt) cc_final: 0.7087 (pp) REVERT: A 1144 GLU cc_start: 0.7477 (pt0) cc_final: 0.7183 (pt0) REVERT: A 1155 ILE cc_start: 0.7670 (mm) cc_final: 0.7458 (mt) REVERT: A 1177 LYS cc_start: 0.7579 (ttpt) cc_final: 0.7379 (ttpp) REVERT: A 1184 THR cc_start: 0.7753 (t) cc_final: 0.7523 (t) REVERT: A 1186 LYS cc_start: 0.7340 (mmtm) cc_final: 0.7005 (mmtm) REVERT: A 1238 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7251 (mptt) REVERT: A 1243 LYS cc_start: 0.7112 (mttp) cc_final: 0.6896 (mtpp) REVERT: A 1296 GLU cc_start: 0.7617 (tt0) cc_final: 0.7021 (pt0) REVERT: A 1311 LEU cc_start: 0.7272 (mt) cc_final: 0.7026 (mt) REVERT: A 1323 ARG cc_start: 0.6117 (ptt90) cc_final: 0.5809 (ptt90) outliers start: 4 outliers final: 2 residues processed: 179 average time/residue: 0.6483 time to fit residues: 125.4468 Evaluate side-chains 155 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 1417 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 971 GLN A1346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.232593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.190411 restraints weight = 35896.551| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 4.40 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4266 r_free = 0.4266 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4266 r_free = 0.4266 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13503 Z= 0.209 Angle : 0.643 14.072 18840 Z= 0.347 Chirality : 0.045 0.254 2114 Planarity : 0.005 0.050 1895 Dihedral : 21.077 122.978 3245 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.18 % Allowed : 8.35 % Favored : 90.47 % 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: -0.21 (0.24), residues: 1195 helix: 0.73 (0.23), residues: 473 sheet: -0.82 (0.43), residues: 131 loop : -0.63 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 692 TYR 0.016 0.002 TYR A 400 PHE 0.021 0.002 PHE A1095 TRP 0.021 0.002 TRP A1005 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (13503) covalent geometry : angle 0.64293 / 0.35 (18840) hydrogen bonds : bond 0.05681 / 3.89 ( 516) hydrogen bonds : angle 4.39268 / 3.09 ( 1325) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7541 (tp30) cc_final: 0.7240 (tp30) REVERT: A 64 TYR cc_start: 0.7894 (m-80) cc_final: 0.7693 (m-80) REVERT: A 201 PHE cc_start: 0.7273 (t80) cc_final: 0.6955 (t80) REVERT: A 317 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6407 (mm-30) REVERT: A 350 ARG cc_start: 0.6454 (ttp-110) cc_final: 0.6099 (mtm-85) REVERT: A 1332 ASP cc_start: 0.6007 (OUTLIER) cc_final: 0.5772 (p0) outliers start: 13 outliers final: 6 residues processed: 165 average time/residue: 0.6104 time to fit residues: 108.6315 Evaluate side-chains 146 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 283 GLN A 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.231698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.175213 restraints weight = 39305.414| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.72 r_work: 0.3832 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13503 Z= 0.182 Angle : 0.587 12.039 18840 Z= 0.320 Chirality : 0.042 0.243 2114 Planarity : 0.005 0.065 1895 Dihedral : 20.937 121.928 3239 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.54 % Allowed : 12.07 % Favored : 86.39 % 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: -0.20 (0.24), residues: 1195 helix: 0.72 (0.23), residues: 472 sheet: -0.57 (0.43), residues: 134 loop : -0.67 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1408 TYR 0.013 0.002 TYR A1361 PHE 0.023 0.002 PHE A1102 TRP 0.039 0.002 TRP A 528 HIS 0.005 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (13503) covalent geometry : angle 0.58691 / 0.32 (18840) hydrogen bonds : bond 0.05169 / 3.50 ( 516) hydrogen bonds : angle 4.27375 / 3.02 ( 1325) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7989 (ttm170) REVERT: A 201 PHE cc_start: 0.7587 (t80) cc_final: 0.7170 (t80) REVERT: A 317 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6883 (mm-30) outliers start: 17 outliers final: 8 residues processed: 156 average time/residue: 0.6319 time to fit residues: 106.0929 Evaluate side-chains 152 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 107 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 chunk 39 optimal weight: 40.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 283 GLN A 944 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.230524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.184745 restraints weight = 39950.361| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 5.10 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4176 r_free = 0.4176 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4176 r_free = 0.4176 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13503 Z= 0.190 Angle : 0.606 12.925 18840 Z= 0.330 Chirality : 0.043 0.254 2114 Planarity : 0.005 0.100 1895 Dihedral : 20.910 120.973 3239 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.09 % Allowed : 13.16 % Favored : 84.75 % 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: -0.27 (0.24), residues: 1195 helix: 0.63 (0.23), residues: 474 sheet: -0.73 (0.42), residues: 139 loop : -0.63 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 381 TYR 0.019 0.002 TYR A 532 PHE 0.025 0.002 PHE A1024 TRP 0.052 0.002 TRP A 528 HIS 0.007 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (13503) covalent geometry : angle 0.60648 / 0.33 (18840) hydrogen bonds : bond 0.04872 / 3.32 ( 516) hydrogen bonds : angle 4.23081 / 2.99 ( 1325) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7559 (tp30) cc_final: 0.7171 (tp30) REVERT: A 201 PHE cc_start: 0.7307 (t80) cc_final: 0.6864 (t80) REVERT: A 317 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6315 (mm-30) REVERT: A 1132 GLU cc_start: 0.6793 (mp0) cc_final: 0.6243 (mp0) REVERT: A 1322 SER cc_start: 0.6803 (OUTLIER) cc_final: 0.6570 (m) outliers start: 23 outliers final: 8 residues processed: 165 average time/residue: 0.6036 time to fit residues: 107.3558 Evaluate side-chains 149 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 116 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 108 optimal weight: 0.0030 chunk 103 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 126 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 283 GLN A1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.231650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.183488 restraints weight = 31577.578| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.71 r_work: 0.3802 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13503 Z= 0.151 Angle : 0.561 12.289 18840 Z= 0.308 Chirality : 0.041 0.255 2114 Planarity : 0.004 0.055 1895 Dihedral : 20.821 120.711 3239 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.81 % Allowed : 14.43 % Favored : 83.76 % 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 (0.24), residues: 1195 helix: 0.79 (0.24), residues: 470 sheet: -0.41 (0.44), residues: 127 loop : -0.68 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 381 TYR 0.018 0.001 TYR A1239 PHE 0.017 0.001 PHE A1024 TRP 0.030 0.002 TRP A 528 HIS 0.009 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (13503) covalent geometry : angle 0.56051 / 0.31 (18840) hydrogen bonds : bond 0.04486 / 3.03 ( 516) hydrogen bonds : angle 4.13407 / 2.94 ( 1325) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8133 (ttm170) REVERT: A 201 PHE cc_start: 0.7568 (t80) cc_final: 0.7108 (t80) REVERT: A 265 PHE cc_start: 0.5124 (m-80) cc_final: 0.4626 (m-80) REVERT: A 317 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6834 (mm-30) REVERT: A 1130 TYR cc_start: 0.7653 (m-10) cc_final: 0.7312 (m-10) REVERT: A 1132 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7116 (mm-30) REVERT: A 1322 SER cc_start: 0.6902 (OUTLIER) cc_final: 0.6661 (m) outliers start: 20 outliers final: 11 residues processed: 159 average time/residue: 0.6069 time to fit residues: 104.1775 Evaluate side-chains 162 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain A residue 1216 LYS Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 77 optimal weight: 0.3980 chunk 57 optimal weight: 40.0000 chunk 53 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A1108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.231361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.183434 restraints weight = 30142.992| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.45 r_work: 0.3816 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13503 Z= 0.148 Angle : 0.559 12.428 18840 Z= 0.308 Chirality : 0.041 0.254 2114 Planarity : 0.004 0.055 1895 Dihedral : 20.739 120.228 3239 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.27 % Allowed : 14.25 % Favored : 83.48 % 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: -0.12 (0.24), residues: 1195 helix: 0.80 (0.24), residues: 470 sheet: -0.47 (0.45), residues: 117 loop : -0.65 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 381 TYR 0.014 0.001 TYR A1239 PHE 0.017 0.001 PHE A1024 TRP 0.029 0.002 TRP A 660 HIS 0.009 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (13503) covalent geometry : angle 0.55914 / 0.31 (18840) hydrogen bonds : bond 0.04397 / 2.98 ( 516) hydrogen bonds : angle 4.10468 / 2.91 ( 1325) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7565 (tp30) cc_final: 0.7117 (tp30) REVERT: A 64 TYR cc_start: 0.8247 (m-80) cc_final: 0.8042 (m-80) REVERT: A 201 PHE cc_start: 0.7567 (t80) cc_final: 0.7102 (t80) REVERT: A 317 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6822 (mm-30) REVERT: A 945 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7464 (mt) REVERT: A 1130 TYR cc_start: 0.7655 (m-10) cc_final: 0.7264 (m-10) REVERT: A 1132 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: A 1322 SER cc_start: 0.6937 (OUTLIER) cc_final: 0.6711 (m) outliers start: 25 outliers final: 16 residues processed: 160 average time/residue: 0.6273 time to fit residues: 108.1436 Evaluate side-chains 163 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain A residue 1216 LYS Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1388 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A1108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.227402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.181252 restraints weight = 37697.887| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 4.74 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 13503 Z= 0.297 Angle : 0.694 12.273 18840 Z= 0.373 Chirality : 0.048 0.253 2114 Planarity : 0.005 0.056 1895 Dihedral : 20.813 121.294 3239 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.54 % Allowed : 14.52 % Favored : 82.94 % 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: -0.57 (0.24), residues: 1195 helix: 0.32 (0.23), residues: 470 sheet: -1.00 (0.41), residues: 138 loop : -0.71 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 381 TYR 0.023 0.002 TYR A1361 PHE 0.019 0.002 PHE A1254 TRP 0.036 0.003 TRP A 660 HIS 0.007 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.30 (13503) covalent geometry : angle 0.69358 / 0.37 (18840) hydrogen bonds : bond 0.05946 / 4.02 ( 516) hydrogen bonds : angle 4.39379 / 3.12 ( 1325) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7372 (t80) cc_final: 0.6955 (t80) REVERT: A 317 GLU cc_start: 0.6578 (mm-30) cc_final: 0.6367 (mm-30) REVERT: A 1243 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8085 (mmmm) REVERT: A 1374 VAL cc_start: 0.8386 (m) cc_final: 0.7994 (t) outliers start: 28 outliers final: 14 residues processed: 172 average time/residue: 0.6290 time to fit residues: 117.1260 Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1243 LYS Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 0.0980 chunk 99 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 283 GLN A 337 GLN A 995 GLN A1108 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.229859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.181018 restraints weight = 35488.358| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 4.34 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4153 r_free = 0.4153 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4153 r_free = 0.4153 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13503 Z= 0.138 Angle : 0.582 11.899 18840 Z= 0.320 Chirality : 0.041 0.258 2114 Planarity : 0.004 0.055 1895 Dihedral : 20.771 120.803 3239 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.81 % Allowed : 15.97 % Favored : 82.21 % 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: -0.30 (0.24), residues: 1195 helix: 0.61 (0.24), residues: 469 sheet: -0.71 (0.43), residues: 126 loop : -0.67 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 381 TYR 0.018 0.001 TYR A1239 PHE 0.038 0.001 PHE A 669 TRP 0.033 0.002 TRP A 528 HIS 0.009 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (13503) covalent geometry : angle 0.58233 / 0.32 (18840) hydrogen bonds : bond 0.04337 / 2.90 ( 516) hydrogen bonds : angle 4.17134 / 2.96 ( 1325) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7519 (ttm170) REVERT: A 201 PHE cc_start: 0.7334 (t80) cc_final: 0.6941 (t80) REVERT: A 317 GLU cc_start: 0.6531 (mm-30) cc_final: 0.6316 (mm-30) REVERT: A 1132 GLU cc_start: 0.6655 (mm-30) cc_final: 0.6243 (mm-30) REVERT: A 1145 ARG cc_start: 0.7078 (mpt90) cc_final: 0.6678 (mpt90) REVERT: A 1243 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8206 (mmmm) outliers start: 20 outliers final: 12 residues processed: 166 average time/residue: 0.6198 time to fit residues: 111.1481 Evaluate side-chains 164 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1243 LYS Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.0270 chunk 127 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 337 GLN A1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.229119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.179998 restraints weight = 34034.833| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 4.37 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13503 Z= 0.174 Angle : 0.606 14.636 18840 Z= 0.325 Chirality : 0.043 0.256 2114 Planarity : 0.004 0.055 1895 Dihedral : 20.744 120.731 3239 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.63 % Allowed : 16.61 % Favored : 81.76 % 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: -0.30 (0.24), residues: 1195 helix: 0.64 (0.24), residues: 471 sheet: -0.66 (0.44), residues: 126 loop : -0.71 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 381 TYR 0.019 0.001 TYR A 186 PHE 0.030 0.002 PHE A1102 TRP 0.035 0.002 TRP A 528 HIS 0.007 0.001 HIS A1033 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (13503) covalent geometry : angle 0.60624 / 0.32 (18840) hydrogen bonds : bond 0.04569 / 3.08 ( 516) hydrogen bonds : angle 4.14293 / 2.95 ( 1325) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7578 (ttm170) REVERT: A 136 MET cc_start: 0.6843 (ttp) cc_final: 0.6533 (ttm) REVERT: A 201 PHE cc_start: 0.7376 (t80) cc_final: 0.6983 (t80) REVERT: A 317 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6338 (mm-30) REVERT: A 995 GLN cc_start: 0.6745 (mp10) cc_final: 0.6102 (mp10) REVERT: A 1132 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6268 (mm-30) REVERT: A 1145 ARG cc_start: 0.7125 (mpt90) cc_final: 0.6668 (mpt90) REVERT: A 1243 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8190 (mmmm) outliers start: 18 outliers final: 13 residues processed: 162 average time/residue: 0.6008 time to fit residues: 105.3321 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1243 LYS Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 125 optimal weight: 60.0000 chunk 121 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 337 GLN A1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.225906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.176073 restraints weight = 30851.905| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 4.28 r_work: 0.3680 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 13503 Z= 0.363 Angle : 0.756 14.707 18840 Z= 0.403 Chirality : 0.052 0.257 2114 Planarity : 0.005 0.056 1895 Dihedral : 20.864 121.894 3239 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.72 % Allowed : 16.61 % Favored : 81.67 % 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: -0.69 (0.24), residues: 1195 helix: 0.29 (0.24), residues: 467 sheet: -1.04 (0.41), residues: 138 loop : -0.84 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 381 TYR 0.026 0.003 TYR A 186 PHE 0.023 0.002 PHE A1254 TRP 0.037 0.003 TRP A 528 HIS 0.010 0.002 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.36 (13503) covalent geometry : angle 0.75644 / 0.40 (18840) hydrogen bonds : bond 0.06264 / 4.24 ( 516) hydrogen bonds : angle 4.49407 / 3.20 ( 1325) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 136 MET cc_start: 0.7230 (ttp) cc_final: 0.6882 (ttm) REVERT: A 201 PHE cc_start: 0.7691 (t80) cc_final: 0.7228 (t80) REVERT: A 208 ARG cc_start: 0.5316 (ptt-90) cc_final: 0.5079 (ptp90) REVERT: A 232 TYR cc_start: 0.6673 (t80) cc_final: 0.6212 (m-80) REVERT: A 317 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6890 (mm-30) REVERT: A 995 GLN cc_start: 0.7315 (mp10) cc_final: 0.7096 (mp10) REVERT: A 1102 PHE cc_start: 0.7450 (t80) cc_final: 0.7213 (t80) REVERT: A 1132 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 1145 ARG cc_start: 0.7563 (mpt90) cc_final: 0.7029 (mpt90) REVERT: A 1243 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8210 (mmmm) outliers start: 19 outliers final: 13 residues processed: 158 average time/residue: 0.6312 time to fit residues: 107.4253 Evaluate side-chains 158 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1243 LYS Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1388 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 53 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 94 optimal weight: 0.0870 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 337 GLN A1108 HIS A1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.229307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.169235 restraints weight = 41367.885| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.93 r_work: 0.3786 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13503 Z= 0.147 Angle : 0.620 18.608 18840 Z= 0.331 Chirality : 0.043 0.260 2114 Planarity : 0.004 0.055 1895 Dihedral : 20.812 121.559 3239 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.36 % Allowed : 17.15 % Favored : 81.49 % 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 (0.24), residues: 1195 helix: 0.59 (0.24), residues: 470 sheet: -1.05 (0.41), residues: 145 loop : -0.71 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 381 TYR 0.020 0.001 TYR A1239 PHE 0.016 0.001 PHE A 335 TRP 0.037 0.002 TRP A 528 HIS 0.014 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (13503) covalent geometry : angle 0.61987 / 0.33 (18840) hydrogen bonds : bond 0.04384 / 2.94 ( 516) hydrogen bonds : angle 4.20373 / 3.00 ( 1325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4980.74 seconds wall clock time: 85 minutes 28.86 seconds (5128.86 seconds total)