Starting phenix.real_space_refine on Fri Jul 3 07:54:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmh_37652/07_2026/8wmh_37652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmh_37652/07_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_37652/07_2026/8wmh_37652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmh_37652/07_2026/8wmh_37652.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmh_37652/07_2026/8wmh_37652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmh_37652/07_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-dev-6108/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: 4.37, per 1000 atoms: 0.34 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: 1.13 Conformation dependent library (CDL) restraints added in 796.6 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: 1.45 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: 3.11 Time building geometry restraints manager: 1.64 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: 18316 1.41 - 2.82: 432 2.82 - 4.23: 72 4.23 - 5.64: 17 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=" N LYS A1417 " pdb=" CA LYS A1417 " pdb=" C LYS A1417 " ideal model delta sigma weight residual 110.20 115.76 -5.56 1.58e+00 4.01e-01 1.24e+01 angle pdb=" O4' DC C 48 " pdb=" C4' DC C 48 " pdb=" C3' DC C 48 " ideal model delta sigma weight residual 106.00 104.02 1.98 6.00e-01 2.78e+00 1.08e+01 angle pdb=" N GLU A 72 " pdb=" CA GLU A 72 " pdb=" CB GLU A 72 " ideal model delta sigma weight residual 110.22 115.13 -4.91 1.54e+00 4.22e-01 1.02e+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: 1614 0.041 - 0.081: 374 0.081 - 0.122: 111 0.122 - 0.163: 12 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: 1.820 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.060 ------------------------------------------------------------------------------- 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= 0.232 Angle : 0.539 7.056 18840 Z= 0.366 Chirality : 0.040 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 0.00337 / 0.23 (13503) covalent geometry : angle 0.53884 / 0.37 (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 : 0.345 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 1241 ASP cc_start: 0.7256 (m-30) cc_final: 0.7006 (m-30) REVERT: A 1243 LYS cc_start: 0.7112 (mttp) cc_final: 0.6782 (mtmm) 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: 0.6509 time to fit residues: 126.1143 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 : 0.394 ------------------------------------------------------------------------------- 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: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 50.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A1346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.233433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.189467 restraints weight = 36114.668| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 4.74 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4246 r_free = 0.4246 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4246 r_free = 0.4246 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13503 Z= 0.204 Angle : 0.613 14.544 18840 Z= 0.336 Chirality : 0.044 0.229 2114 Planarity : 0.005 0.050 1895 Dihedral : 21.096 123.796 3245 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.18 % Allowed : 8.26 % Favored : 90.56 % 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: -0.15 (0.24), residues: 1195 helix: 0.80 (0.23), residues: 473 sheet: -0.73 (0.46), residues: 119 loop : -0.64 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 692 TYR 0.020 0.002 TYR A 400 PHE 0.028 0.002 PHE A1095 TRP 0.019 0.002 TRP A1005 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (13503) covalent geometry : angle 0.61293 / 0.34 (18840) hydrogen bonds : bond 0.05393 / 3.69 ( 516) hydrogen bonds : angle 4.35600 / 3.07 ( 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 171 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.5308 (mmm) cc_final: 0.5057 (mmm) REVERT: A 60 GLU cc_start: 0.7601 (tp30) cc_final: 0.7234 (tp30) REVERT: A 64 TYR cc_start: 0.7925 (m-80) cc_final: 0.7685 (m-80) REVERT: A 201 PHE cc_start: 0.7303 (t80) cc_final: 0.6968 (t80) REVERT: A 280 LYS cc_start: 0.7600 (ttpt) cc_final: 0.7391 (ttmm) REVERT: A 317 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6348 (mm-30) REVERT: A 656 MET cc_start: -0.1318 (pmm) cc_final: -0.1524 (pmm) REVERT: A 1332 ASP cc_start: 0.6020 (OUTLIER) cc_final: 0.5762 (p0) outliers start: 13 outliers final: 6 residues processed: 163 average time/residue: 0.6991 time to fit residues: 123.2041 Evaluate side-chains 151 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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: 6.9990 chunk 50 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 0.0170 chunk 105 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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 = 0.4717 r_free = 0.4717 target = 0.231174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174009 restraints weight = 38957.593| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.76 r_work: 0.3818 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2250 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= 0.198 Angle : 0.606 11.525 18840 Z= 0.333 Chirality : 0.043 0.218 2114 Planarity : 0.005 0.059 1895 Dihedral : 20.969 122.096 3239 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.91 % Allowed : 11.43 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1195 helix: 0.71 (0.23), residues: 473 sheet: -0.80 (0.43), residues: 129 loop : -0.70 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 381 TYR 0.016 0.002 TYR A1361 PHE 0.030 0.002 PHE A1024 TRP 0.053 0.002 TRP A 528 HIS 0.006 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (13503) covalent geometry : angle 0.60602 / 0.33 (18840) hydrogen bonds : bond 0.05285 / 3.56 ( 516) hydrogen bonds : angle 4.28521 / 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 180 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7980 (ttm170) REVERT: A 201 PHE cc_start: 0.7603 (t80) cc_final: 0.7137 (t80) REVERT: A 280 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7770 (ttmm) REVERT: A 317 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6872 (mm-30) REVERT: A 1322 SER cc_start: 0.6720 (OUTLIER) cc_final: 0.6422 (m) outliers start: 21 outliers final: 9 residues processed: 169 average time/residue: 0.6979 time to fit residues: 127.3144 Evaluate side-chains 155 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 981 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 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: 0.5980 chunk 70 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 0.1980 chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 39 optimal weight: 40.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4715 r_free = 0.4715 target = 0.230958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.173402 restraints weight = 39838.627| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 3.74 r_work: 0.3812 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 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 = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2609 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= 0.184 Angle : 0.592 13.055 18840 Z= 0.324 Chirality : 0.042 0.219 2114 Planarity : 0.004 0.055 1895 Dihedral : 20.951 121.482 3239 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.09 % Allowed : 13.25 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1195 helix: 0.70 (0.24), residues: 469 sheet: -0.56 (0.43), residues: 134 loop : -0.67 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 381 TYR 0.013 0.002 TYR A1361 PHE 0.017 0.002 PHE A 425 TRP 0.037 0.002 TRP A 528 HIS 0.007 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (13503) covalent geometry : angle 0.59156 / 0.32 (18840) hydrogen bonds : bond 0.04735 / 3.20 ( 516) hydrogen bonds : angle 4.26141 / 3.01 ( 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 176 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7554 (t80) cc_final: 0.7033 (t80) REVERT: A 280 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7783 (ttmm) REVERT: A 317 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6782 (mm-30) REVERT: A 1132 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: A 1230 ASP cc_start: 0.7414 (t0) cc_final: 0.7206 (m-30) REVERT: A 1322 SER cc_start: 0.6885 (OUTLIER) cc_final: 0.6662 (m) outliers start: 23 outliers final: 11 residues processed: 164 average time/residue: 0.7322 time to fit residues: 129.1555 Evaluate side-chains 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 1132 GLU Chi-restraints excluded: chain A residue 1142 ASN Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1216 LYS 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: 1.9990 chunk 114 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 108 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 126 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 79 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4715 r_free = 0.4715 target = 0.231426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.183784 restraints weight = 31364.732| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.80 r_work: 0.3783 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2825 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 : 0.551 12.650 18840 Z= 0.306 Chirality : 0.041 0.219 2114 Planarity : 0.004 0.056 1895 Dihedral : 20.858 121.071 3239 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.18 % Allowed : 14.43 % Favored : 83.39 % 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: -0.10 (0.24), residues: 1195 helix: 0.83 (0.24), residues: 470 sheet: -0.45 (0.43), residues: 134 loop : -0.65 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1323 TYR 0.016 0.001 TYR A1239 PHE 0.013 0.001 PHE A 990 TRP 0.030 0.002 TRP A 660 HIS 0.008 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (13503) covalent geometry : angle 0.55082 / 0.31 (18840) hydrogen bonds : bond 0.04347 / 2.93 ( 516) hydrogen bonds : angle 4.14501 / 2.93 ( 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 181 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8129 (ttm170) REVERT: A 86 TYR cc_start: 0.8323 (t80) cc_final: 0.8092 (t80) REVERT: A 201 PHE cc_start: 0.7570 (t80) cc_final: 0.7086 (t80) REVERT: A 280 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7808 (ttmm) REVERT: A 317 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6877 (mm-30) REVERT: A 1130 TYR cc_start: 0.7717 (m-80) cc_final: 0.7340 (m-10) REVERT: A 1132 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 1322 SER cc_start: 0.6904 (OUTLIER) cc_final: 0.6695 (m) outliers start: 24 outliers final: 13 residues processed: 165 average time/residue: 0.7446 time to fit residues: 132.3336 Evaluate side-chains 163 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 104 ARG Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1180 ILE 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 Chi-restraints excluded: chain A residue 1388 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 57 optimal weight: 40.0000 chunk 53 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4701 r_free = 0.4701 target = 0.230357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.182160 restraints weight = 29927.677| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 3.64 r_work: 0.3790 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13503 Z= 0.181 Angle : 0.581 12.213 18840 Z= 0.319 Chirality : 0.042 0.219 2114 Planarity : 0.004 0.056 1895 Dihedral : 20.778 120.570 3239 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.09 % Allowed : 14.61 % Favored : 83.30 % 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: -0.23 (0.24), residues: 1195 helix: 0.71 (0.24), residues: 470 sheet: -0.90 (0.41), residues: 141 loop : -0.60 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 381 TYR 0.013 0.002 TYR A1372 PHE 0.014 0.001 PHE A 990 TRP 0.028 0.002 TRP A 660 HIS 0.008 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (13503) covalent geometry : angle 0.58061 / 0.32 (18840) hydrogen bonds : bond 0.04616 / 3.13 ( 516) hydrogen bonds : angle 4.18158 / 2.97 ( 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 185 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7990 (m-80) cc_final: 0.7384 (m-80) REVERT: A 201 PHE cc_start: 0.7573 (t80) cc_final: 0.7078 (t80) REVERT: A 280 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7801 (ttmm) REVERT: A 317 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6875 (mm-30) REVERT: A 1102 PHE cc_start: 0.6565 (t80) cc_final: 0.6337 (t80) REVERT: A 1132 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7035 (mm-30) outliers start: 23 outliers final: 14 residues processed: 170 average time/residue: 0.7088 time to fit residues: 129.7938 Evaluate side-chains 172 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 181 HIS Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 945 ILE 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 1194 LEU Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 74 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 49 optimal weight: 0.0060 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4710 r_free = 0.4710 target = 0.230848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.170856 restraints weight = 38355.990| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 3.69 r_work: 0.3819 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13503 Z= 0.139 Angle : 0.552 12.313 18840 Z= 0.304 Chirality : 0.040 0.219 2114 Planarity : 0.004 0.055 1895 Dihedral : 20.741 120.153 3239 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.72 % Allowed : 15.34 % 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: -0.18 (0.24), residues: 1195 helix: 0.80 (0.24), residues: 470 sheet: -1.19 (0.40), residues: 140 loop : -0.53 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 381 TYR 0.018 0.001 TYR A 186 PHE 0.039 0.001 PHE A 669 TRP 0.031 0.001 TRP A 528 HIS 0.011 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (13503) covalent geometry : angle 0.55249 / 0.30 (18840) hydrogen bonds : bond 0.04113 / 2.78 ( 516) hydrogen bonds : angle 4.07512 / 2.89 ( 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 176 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8024 (ttm170) REVERT: A 201 PHE cc_start: 0.7494 (t80) cc_final: 0.6990 (t80) REVERT: A 280 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7766 (ttmm) REVERT: A 317 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6840 (mm-30) REVERT: A 1102 PHE cc_start: 0.6563 (t80) cc_final: 0.6270 (t80) REVERT: A 1380 TYR cc_start: 0.7438 (m-80) cc_final: 0.7095 (m-80) outliers start: 19 outliers final: 7 residues processed: 163 average time/residue: 0.7046 time to fit residues: 123.6445 Evaluate side-chains 159 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 945 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1236 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 46 optimal weight: 0.2980 chunk 44 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 40 optimal weight: 50.0000 chunk 11 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 178 ASN A 283 GLN A1108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.230315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.182991 restraints weight = 35698.557| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 4.88 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4177 r_free = 0.4177 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4177 r_free = 0.4177 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13503 Z= 0.164 Angle : 0.572 14.429 18840 Z= 0.313 Chirality : 0.041 0.218 2114 Planarity : 0.004 0.056 1895 Dihedral : 20.722 119.759 3239 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.91 % Allowed : 15.70 % Favored : 82.40 % 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: -0.25 (0.24), residues: 1195 helix: 0.74 (0.24), residues: 471 sheet: -1.30 (0.41), residues: 123 loop : -0.56 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 381 TYR 0.013 0.001 TYR A1239 PHE 0.014 0.001 PHE A 990 TRP 0.030 0.002 TRP A 528 HIS 0.010 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (13503) covalent geometry : angle 0.57167 / 0.31 (18840) hydrogen bonds : bond 0.04342 / 2.94 ( 516) hydrogen bonds : angle 4.11512 / 2.93 ( 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 182 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7446 (ttm170) REVERT: A 79 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6780 (mm-30) REVERT: A 201 PHE cc_start: 0.7376 (t80) cc_final: 0.6929 (t80) REVERT: A 280 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7546 (ttmm) REVERT: A 317 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6315 (mm-30) REVERT: A 1380 TYR cc_start: 0.6685 (m-80) cc_final: 0.6392 (m-80) outliers start: 21 outliers final: 13 residues processed: 167 average time/residue: 0.6812 time to fit residues: 122.6971 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 364 ARG Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1184 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 283 GLN A 960 ASN A1108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.228083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.178596 restraints weight = 33731.524| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 4.95 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13503 Z= 0.257 Angle : 0.654 14.066 18840 Z= 0.354 Chirality : 0.046 0.217 2114 Planarity : 0.005 0.056 1895 Dihedral : 20.778 119.302 3239 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.63 % Allowed : 16.70 % 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: -0.43 (0.24), residues: 1195 helix: 0.48 (0.24), residues: 470 sheet: -0.72 (0.44), residues: 126 loop : -0.73 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 381 TYR 0.019 0.002 TYR A 295 PHE 0.029 0.002 PHE A1102 TRP 0.030 0.002 TRP A 528 HIS 0.008 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.26 (13503) covalent geometry : angle 0.65356 / 0.35 (18840) hydrogen bonds : bond 0.05231 / 3.53 ( 516) hydrogen bonds : angle 4.31598 / 3.08 ( 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 180 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7429 (t80) cc_final: 0.6993 (t80) REVERT: A 280 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7552 (ttmm) outliers start: 18 outliers final: 12 residues processed: 168 average time/residue: 0.5946 time to fit residues: 107.8610 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 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 945 ILE 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 1236 ILE Chi-restraints excluded: chain A residue 1311 LEU 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: 50.0000 chunk 121 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 77 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 39 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 283 GLN A 337 GLN A1108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.229082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.179550 restraints weight = 31048.857| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 4.06 r_work: 0.3755 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.004 0.051 13503 Z= 0.181 Angle : 0.611 14.238 18840 Z= 0.332 Chirality : 0.043 0.217 2114 Planarity : 0.005 0.087 1895 Dihedral : 20.784 119.022 3239 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.45 % Allowed : 17.33 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1195 helix: 0.57 (0.24), residues: 470 sheet: -1.13 (0.43), residues: 123 loop : -0.72 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A1028 TYR 0.045 0.002 TYR A1380 PHE 0.014 0.001 PHE A 990 TRP 0.033 0.002 TRP A 528 HIS 0.014 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (13503) covalent geometry : angle 0.61101 / 0.33 (18840) hydrogen bonds : bond 0.04529 / 3.03 ( 516) hydrogen bonds : angle 4.26092 / 3.03 ( 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 173 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8140 (ttm170) REVERT: A 201 PHE cc_start: 0.7592 (t80) cc_final: 0.7098 (t80) REVERT: A 232 TYR cc_start: 0.6533 (t80) cc_final: 0.6054 (m-80) REVERT: A 280 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7846 (ttmm) REVERT: A 1102 PHE cc_start: 0.7265 (t80) cc_final: 0.6983 (t80) REVERT: A 1380 TYR cc_start: 0.7179 (m-80) cc_final: 0.6946 (m-80) outliers start: 16 outliers final: 13 residues processed: 162 average time/residue: 0.7054 time to fit residues: 123.2425 Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 1103 THR Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1322 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 53 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 283 GLN A 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.228917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.183407 restraints weight = 41298.368| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 5.69 r_work: 0.3676 rms_B_bonded: 5.67 restraints_weight: 2.0000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13503 Z= 0.170 Angle : 0.610 14.392 18840 Z= 0.330 Chirality : 0.043 0.216 2114 Planarity : 0.004 0.081 1895 Dihedral : 20.774 118.839 3239 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.45 % Allowed : 17.06 % 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: -0.38 (0.24), residues: 1195 helix: 0.61 (0.24), residues: 470 sheet: -0.92 (0.43), residues: 133 loop : -0.74 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A1028 TYR 0.031 0.001 TYR A1380 PHE 0.014 0.001 PHE A 990 TRP 0.032 0.002 TRP A 528 HIS 0.017 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (13503) covalent geometry : angle 0.60965 / 0.33 (18840) hydrogen bonds : bond 0.04424 / 2.96 ( 516) hydrogen bonds : angle 4.20966 / 3.00 ( 1325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5917.60 seconds wall clock time: 101 minutes 35.68 seconds (6095.68 seconds total)