Starting phenix.real_space_refine on Thu Jul 31 01:32:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmh_37652/07_2025/8wmh_37652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmh_37652/07_2025/8wmh_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_2025/8wmh_37652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmh_37652/07_2025/8wmh_37652.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmh_37652/07_2025/8wmh_37652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmh_37652/07_2025/8wmh_37652.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.94, per 1000 atoms: 0.92 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: 3.14 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 5.51 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: 7.21 Time building geometry restraints manager: 3.76 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=" 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=" C ARG A1122 " pdb=" N VAL A1123 " ideal model delta sigma weight residual 1.333 1.303 0.031 1.46e-02 4.69e+03 4.39e+00 bond pdb=" CA ARG A 692 " pdb=" CB ARG A 692 " ideal model delta sigma weight residual 1.529 1.496 0.032 1.58e-02 4.01e+03 4.22e+00 bond pdb=" C GLY A1392 " pdb=" N GLU A1393 " ideal model delta sigma weight residual 1.334 1.310 0.024 1.33e-02 5.65e+03 3.30e+00 ... (remaining 13498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 18331 1.41 - 2.82: 416 2.82 - 4.23: 73 4.23 - 5.64: 18 5.64 - 7.06: 2 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=" 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=" 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 angle pdb=" N LYS A 272 " pdb=" CA LYS A 272 " pdb=" C LYS A 272 " ideal model delta sigma weight residual 114.75 110.93 3.82 1.26e+00 6.30e-01 9.19e+00 angle pdb=" O3' DA E 16 " pdb=" C3' DA E 16 " pdb=" C2' DA E 16 " ideal model delta sigma weight residual 111.50 107.02 4.48 1.50e+00 4.44e-01 8.91e+00 ... (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 - 0.033: 1496 0.033 - 0.067: 441 0.067 - 0.100: 116 0.100 - 0.134: 53 0.134 - 0.167: 8 Chirality restraints: 2114 Sorted by residual: 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 chirality pdb=" CA LYS A1417 " pdb=" N LYS A1417 " pdb=" C LYS A1417 " pdb=" CB LYS A1417 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.53e-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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 43.730 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 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= 0.161 Angle : 0.541 7.056 18840 Z= 0.311 Chirality : 0.038 0.167 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.001 TRP A 528 HIS 0.003 0.001 HIS A1033 PHE 0.017 0.001 PHE A 990 TYR 0.012 0.001 TYR A1380 ARG 0.010 0.000 ARG A1028 Details of bonding type rmsd hydrogen bonds : bond 0.15083 ( 516) hydrogen bonds : angle 5.84872 ( 1325) covalent geometry : bond 0.00328 (13503) covalent geometry : angle 0.54070 (18840) *********************** 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 : 1.192 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: 0.7207 (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: 1.4037 time to fit residues: 272.2944 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 : 1.216 ------------------------------------------------------------------------------- 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 110 optimal weight: 0.7980 chunk 99 optimal weight: 0.1980 chunk 55 optimal weight: 50.0000 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 53 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 30.0000 chunk 62 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 287 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.232674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.176018 restraints weight = 40955.256| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.84 r_work: 0.3842 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13503 Z= 0.178 Angle : 0.587 13.765 18840 Z= 0.314 Chirality : 0.041 0.200 2114 Planarity : 0.004 0.051 1895 Dihedral : 20.823 122.396 3245 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.00 % Allowed : 8.26 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1195 helix: 0.91 (0.23), residues: 472 sheet: -0.47 (0.46), residues: 119 loop : -0.62 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 487 HIS 0.004 0.001 HIS A 477 PHE 0.013 0.002 PHE A1102 TYR 0.014 0.001 TYR A1131 ARG 0.009 0.001 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 516) hydrogen bonds : angle 4.27421 ( 1325) covalent geometry : bond 0.00390 (13503) covalent geometry : angle 0.58709 (18840) *********************** 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 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.4836 (mmm) cc_final: 0.4628 (mmm) REVERT: A 69 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.8039 (ttm170) REVERT: A 168 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: A 201 PHE cc_start: 0.7492 (t80) cc_final: 0.7177 (t80) REVERT: A 265 PHE cc_start: 0.3745 (m-80) cc_final: 0.3118 (m-80) REVERT: A 280 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7755 (ttmm) REVERT: A 311 LYS cc_start: 0.7936 (tppt) cc_final: 0.7731 (tppp) REVERT: A 317 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6905 (mm-30) REVERT: A 350 ARG cc_start: 0.6926 (ttp-110) cc_final: 0.6570 (mtm-85) REVERT: A 367 ASP cc_start: 0.7481 (p0) cc_final: 0.7280 (p0) outliers start: 11 outliers final: 4 residues processed: 172 average time/residue: 1.7205 time to fit residues: 321.0615 Evaluate side-chains 150 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 0.0980 chunk 68 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 283 GLN A 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.230066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.180641 restraints weight = 34312.595| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 4.70 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 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 = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13503 Z= 0.198 Angle : 0.589 13.397 18840 Z= 0.316 Chirality : 0.041 0.197 2114 Planarity : 0.004 0.052 1895 Dihedral : 20.773 121.778 3239 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.27 % Allowed : 11.25 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1195 helix: 0.73 (0.24), residues: 471 sheet: -0.48 (0.45), residues: 117 loop : -0.62 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 528 HIS 0.004 0.001 HIS A1034 PHE 0.021 0.002 PHE A1024 TYR 0.013 0.002 TYR A 295 ARG 0.010 0.001 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 516) hydrogen bonds : angle 4.19401 ( 1325) covalent geometry : bond 0.00430 (13503) covalent geometry : angle 0.58870 (18840) *********************** 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 197 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7334 (t80) cc_final: 0.6958 (t80) REVERT: A 265 PHE cc_start: 0.4086 (m-80) cc_final: 0.3513 (m-80) REVERT: A 280 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7534 (ttmm) REVERT: A 317 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6352 (mm-30) outliers start: 25 outliers final: 9 residues processed: 182 average time/residue: 1.5304 time to fit residues: 300.9374 Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 958 SER Chi-restraints excluded: chain A residue 1043 CYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 8 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 55 optimal weight: 40.0000 chunk 39 optimal weight: 30.0000 chunk 35 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4696 r_free = 0.4696 target = 0.229042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.168841 restraints weight = 40259.123| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.90 r_work: 0.3781 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13503 Z= 0.200 Angle : 0.595 13.709 18840 Z= 0.319 Chirality : 0.042 0.195 2114 Planarity : 0.004 0.053 1895 Dihedral : 20.767 120.199 3239 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.63 % Allowed : 13.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1195 helix: 0.63 (0.24), residues: 472 sheet: -0.53 (0.44), residues: 117 loop : -0.67 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 528 HIS 0.003 0.001 HIS A1108 PHE 0.015 0.002 PHE A 990 TYR 0.014 0.002 TYR A 295 ARG 0.006 0.001 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 516) hydrogen bonds : angle 4.14245 ( 1325) covalent geometry : bond 0.00443 (13503) covalent geometry : angle 0.59457 (18840) *********************** 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 193 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8110 (ttm170) REVERT: A 201 PHE cc_start: 0.7600 (t80) cc_final: 0.7171 (t80) REVERT: A 208 ARG cc_start: 0.5435 (ptt-90) cc_final: 0.5230 (ptp90) REVERT: A 265 PHE cc_start: 0.3761 (m-80) cc_final: 0.2823 (m-80) REVERT: A 280 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7822 (ttmt) REVERT: A 317 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6859 (mm-30) outliers start: 29 outliers final: 14 residues processed: 180 average time/residue: 1.3892 time to fit residues: 270.4286 Evaluate side-chains 170 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1103 THR 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 1316 LEU Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1391 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 47 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 118 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 125 optimal weight: 20.0000 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 283 GLN A 685 GLN A1033 HIS A1108 HIS A1346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.230344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.181253 restraints weight = 39314.221| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 5.32 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4152 r_free = 0.4152 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4152 r_free = 0.4152 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13503 Z= 0.139 Angle : 0.528 13.193 18840 Z= 0.287 Chirality : 0.039 0.194 2114 Planarity : 0.003 0.053 1895 Dihedral : 20.702 119.930 3239 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.00 % Allowed : 14.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1195 helix: 0.83 (0.24), residues: 472 sheet: -1.10 (0.40), residues: 142 loop : -0.50 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 528 HIS 0.005 0.001 HIS A1108 PHE 0.014 0.001 PHE A 990 TYR 0.020 0.001 TYR A1134 ARG 0.004 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 516) hydrogen bonds : angle 3.99474 ( 1325) covalent geometry : bond 0.00303 (13503) covalent geometry : angle 0.52768 (18840) *********************** 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: 22 poor density : 159 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7331 (t80) cc_final: 0.6998 (t80) REVERT: A 265 PHE cc_start: 0.4010 (m-80) cc_final: 0.3308 (m-80) REVERT: A 280 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7526 (ttmt) REVERT: A 587 MET cc_start: -0.1329 (mpp) cc_final: -0.2245 (mpp) outliers start: 22 outliers final: 12 residues processed: 170 average time/residue: 1.4521 time to fit residues: 267.1519 Evaluate side-chains 159 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 995 GLN Chi-restraints excluded: chain A residue 1103 THR 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 1311 LEU 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 16 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 283 GLN A 710 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.227627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.177575 restraints weight = 37031.113| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 4.80 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4114 r_free = 0.4114 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4114 r_free = 0.4114 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13503 Z= 0.210 Angle : 0.592 13.235 18840 Z= 0.320 Chirality : 0.042 0.194 2114 Planarity : 0.004 0.054 1895 Dihedral : 20.776 118.868 3239 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.09 % Allowed : 15.06 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.24), residues: 1195 helix: 0.60 (0.24), residues: 473 sheet: -0.67 (0.44), residues: 128 loop : -0.63 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 528 HIS 0.005 0.001 HIS A1033 PHE 0.018 0.001 PHE A1102 TYR 0.021 0.002 TYR A1134 ARG 0.005 0.001 ARG A1252 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 516) hydrogen bonds : angle 4.19076 ( 1325) covalent geometry : bond 0.00467 (13503) covalent geometry : angle 0.59155 (18840) *********************** 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 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7591 (ttm170) REVERT: A 201 PHE cc_start: 0.7264 (t80) cc_final: 0.6860 (t80) REVERT: A 280 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7512 (ttmt) REVERT: A 995 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6443 (mp10) outliers start: 23 outliers final: 14 residues processed: 167 average time/residue: 1.3784 time to fit residues: 249.5295 Evaluate side-chains 164 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 958 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 995 GLN 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 1311 LEU 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 1391 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 126 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 83 optimal weight: 0.0870 chunk 116 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN A1108 HIS A1301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.228196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.180140 restraints weight = 27839.479| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.07 r_work: 0.3813 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 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 = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13503 Z= 0.169 Angle : 0.559 12.598 18840 Z= 0.299 Chirality : 0.040 0.192 2114 Planarity : 0.004 0.054 1895 Dihedral : 20.626 118.426 3239 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.36 % Allowed : 16.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1195 helix: 0.68 (0.24), residues: 473 sheet: -0.80 (0.46), residues: 123 loop : -0.60 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 528 HIS 0.004 0.001 HIS A1033 PHE 0.014 0.001 PHE A 990 TYR 0.019 0.001 TYR A1134 ARG 0.004 0.000 ARG A1028 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 516) hydrogen bonds : angle 4.01430 ( 1325) covalent geometry : bond 0.00373 (13503) covalent geometry : angle 0.55852 (18840) *********************** 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 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7541 (t80) cc_final: 0.7110 (t80) REVERT: A 280 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7792 (ttmt) REVERT: A 1028 ARG cc_start: 0.7177 (ttp80) cc_final: 0.6908 (ttp80) REVERT: A 1102 PHE cc_start: 0.7359 (t80) cc_final: 0.6952 (t80) outliers start: 15 outliers final: 9 residues processed: 159 average time/residue: 1.7243 time to fit residues: 296.2677 Evaluate side-chains 154 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 980 ASP 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 1311 LEU 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 37 optimal weight: 0.3980 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 283 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 = 0.4703 r_free = 0.4703 target = 0.229431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.180104 restraints weight = 33177.884| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 4.22 r_work: 0.3750 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13503 Z= 0.132 Angle : 0.534 12.024 18840 Z= 0.285 Chirality : 0.038 0.190 2114 Planarity : 0.003 0.053 1895 Dihedral : 20.536 117.887 3239 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.54 % Allowed : 16.61 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1195 helix: 0.85 (0.24), residues: 473 sheet: -0.72 (0.47), residues: 125 loop : -0.59 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 528 HIS 0.006 0.001 HIS A1033 PHE 0.014 0.001 PHE A 990 TYR 0.018 0.001 TYR A1134 ARG 0.003 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 516) hydrogen bonds : angle 3.93200 ( 1325) covalent geometry : bond 0.00289 (13503) covalent geometry : angle 0.53360 (18840) *********************** 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 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8144 (ttm170) REVERT: A 280 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7846 (ttmt) REVERT: A 1027 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7823 (tptt) REVERT: A 1028 ARG cc_start: 0.7332 (ttp80) cc_final: 0.7070 (ttp80) REVERT: A 1102 PHE cc_start: 0.7385 (t80) cc_final: 0.6894 (t80) outliers start: 17 outliers final: 10 residues processed: 159 average time/residue: 1.8181 time to fit residues: 311.9655 Evaluate side-chains 159 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1027 LYS Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1311 LEU 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 9 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 38 optimal weight: 0.0010 chunk 47 optimal weight: 6.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 995 GLN A1108 HIS A1301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.227772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.178954 restraints weight = 32595.394| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 3.63 r_work: 0.3759 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13503 Z= 0.186 Angle : 0.578 12.378 18840 Z= 0.308 Chirality : 0.041 0.190 2114 Planarity : 0.004 0.054 1895 Dihedral : 20.607 117.324 3239 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1195 helix: 0.72 (0.24), residues: 472 sheet: -0.97 (0.43), residues: 137 loop : -0.59 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 528 HIS 0.006 0.001 HIS A1033 PHE 0.014 0.001 PHE A 990 TYR 0.017 0.001 TYR A1134 ARG 0.004 0.001 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 516) hydrogen bonds : angle 4.07441 ( 1325) covalent geometry : bond 0.00413 (13503) covalent geometry : angle 0.57839 (18840) *********************** 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 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7539 (t80) cc_final: 0.7022 (t80) REVERT: A 280 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7815 (ttmt) outliers start: 16 outliers final: 12 residues processed: 158 average time/residue: 1.5346 time to fit residues: 261.2073 Evaluate side-chains 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1043 CYS 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 1316 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 66 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 125 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN A 995 GLN A1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.228283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.168286 restraints weight = 42504.680| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.77 r_work: 0.3776 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13503 Z= 0.168 Angle : 0.571 12.247 18840 Z= 0.303 Chirality : 0.040 0.190 2114 Planarity : 0.004 0.054 1895 Dihedral : 20.600 116.928 3239 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.18 % Allowed : 17.70 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1195 helix: 0.70 (0.24), residues: 474 sheet: -0.97 (0.44), residues: 132 loop : -0.63 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 528 HIS 0.013 0.001 HIS A 336 PHE 0.013 0.001 PHE A 990 TYR 0.021 0.001 TYR A 937 ARG 0.006 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 516) hydrogen bonds : angle 4.05988 ( 1325) covalent geometry : bond 0.00372 (13503) covalent geometry : angle 0.57058 (18840) ********************** 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 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7474 (t80) cc_final: 0.7023 (t80) REVERT: A 208 ARG cc_start: 0.5529 (ptp90) cc_final: 0.5229 (ptp90) REVERT: A 280 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7797 (ttmt) REVERT: A 700 LYS cc_start: 0.7579 (ptmt) cc_final: 0.7378 (ptmt) outliers start: 13 outliers final: 10 residues processed: 156 average time/residue: 1.8765 time to fit residues: 314.8480 Evaluate side-chains 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1043 CYS 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 1316 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 10 optimal weight: 0.7980 chunk 76 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 1 optimal weight: 0.0000 chunk 88 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 48 optimal weight: 0.0370 chunk 125 optimal weight: 30.0000 overall best weight: 0.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4727 r_free = 0.4727 target = 0.232000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.175181 restraints weight = 24774.255| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.99 r_work: 0.3891 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13503 Z= 0.109 Angle : 0.532 13.001 18840 Z= 0.284 Chirality : 0.037 0.186 2114 Planarity : 0.003 0.052 1895 Dihedral : 20.487 116.212 3239 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.82 % Allowed : 18.42 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1195 helix: 0.90 (0.24), residues: 473 sheet: -0.79 (0.45), residues: 130 loop : -0.54 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 528 HIS 0.006 0.001 HIS A1033 PHE 0.019 0.001 PHE A1102 TYR 0.016 0.001 TYR A 937 ARG 0.005 0.000 ARG A1323 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 516) hydrogen bonds : angle 3.82356 ( 1325) covalent geometry : bond 0.00234 (13503) covalent geometry : angle 0.53217 (18840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12755.24 seconds wall clock time: 223 minutes 42.06 seconds (13422.06 seconds total)