Starting phenix.real_space_refine on Mon Aug 5 08:44:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/08_2024/8wmh_37652.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/08_2024/8wmh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/08_2024/8wmh_37652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/08_2024/8wmh_37652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/08_2024/8wmh_37652.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/08_2024/8wmh_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 Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 12.59, per 1000 atoms: 0.97 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 - 3.50 Amino acid : False - 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: 6.18 Conformation dependent library (CDL) restraints added in 3.8 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: 4.87 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: 6.90 Time building geometry restraints manager: 6.64 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=" 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: 99.23 - 106.20: 947 106.20 - 113.17: 7356 113.17 - 120.14: 4903 120.14 - 127.11: 5235 127.11 - 134.08: 399 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 51.210 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.790 ------------------------------------------------------------------------------- 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= 0.198 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 1.167 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: 1.3735 time to fit residues: 266.5523 Evaluate side-chains 155 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 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= 0.241 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 *********************** 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 fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8441 (mm) cc_final: 0.8189 (mm) REVERT: A 41 MET cc_start: 0.4974 (mmm) cc_final: 0.4632 (mmm) REVERT: A 63 LYS cc_start: 0.7213 (tptm) cc_final: 0.6764 (tptm) REVERT: A 64 TYR cc_start: 0.7723 (m-80) cc_final: 0.7454 (m-80) REVERT: A 69 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7453 (ttm170) REVERT: A 79 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7188 (mm-30) REVERT: A 164 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7874 (p) REVERT: A 168 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: A 201 PHE cc_start: 0.7265 (t80) cc_final: 0.6906 (t80) REVERT: A 265 PHE cc_start: 0.3610 (m-80) cc_final: 0.2975 (m-80) REVERT: A 280 LYS cc_start: 0.7305 (ttpt) cc_final: 0.6973 (ttmm) REVERT: A 309 LYS cc_start: 0.7850 (mmmm) cc_final: 0.7630 (mmmm) REVERT: A 311 LYS cc_start: 0.7891 (tppt) cc_final: 0.7391 (tppp) REVERT: A 317 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6638 (mm-30) REVERT: A 330 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 350 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.6421 (mtm-85) REVERT: A 365 LYS cc_start: 0.7449 (ptpt) cc_final: 0.7195 (ptpp) REVERT: A 367 ASP cc_start: 0.7135 (p0) cc_final: 0.6482 (p0) REVERT: A 374 GLU cc_start: 0.7099 (tp30) cc_final: 0.6808 (mp0) REVERT: A 381 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7445 (mtt90) REVERT: A 671 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7813 (mmtm) REVERT: A 991 GLU cc_start: 0.7121 (tp30) cc_final: 0.6748 (mm-30) REVERT: A 1013 LEU cc_start: 0.7769 (tp) cc_final: 0.7540 (tm) REVERT: A 1024 PHE cc_start: 0.7413 (t80) cc_final: 0.7150 (t80) REVERT: A 1124 ILE cc_start: 0.7545 (pt) cc_final: 0.7281 (pp) REVERT: A 1133 LYS cc_start: 0.8132 (tttt) cc_final: 0.7736 (tttp) REVERT: A 1177 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7454 (ttpp) REVERT: A 1186 LYS cc_start: 0.7438 (mmtm) cc_final: 0.7105 (mmtm) REVERT: A 1238 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7307 (mptt) REVERT: A 1243 LYS cc_start: 0.7215 (mttp) cc_final: 0.6964 (mtpp) REVERT: A 1296 GLU cc_start: 0.7902 (tt0) cc_final: 0.7408 (pt0) REVERT: A 1323 ARG cc_start: 0.6578 (ptt90) cc_final: 0.6119 (ptt90) REVERT: A 1364 GLU cc_start: 0.7309 (tp30) cc_final: 0.6455 (mp0) REVERT: A 1389 THR cc_start: 0.7510 (m) cc_final: 0.7060 (p) outliers start: 11 outliers final: 4 residues processed: 172 average time/residue: 1.4459 time to fit residues: 269.1096 Evaluate side-chains 153 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER 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 66 optimal weight: 0.3980 chunk 36 optimal weight: 0.0070 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 95 optimal weight: 0.5980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 685 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13503 Z= 0.196 Angle : 0.531 13.188 18840 Z= 0.288 Chirality : 0.039 0.196 2114 Planarity : 0.004 0.052 1895 Dihedral : 20.702 121.807 3239 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.72 % Allowed : 10.89 % Favored : 87.39 % 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: 0.05 (0.24), residues: 1195 helix: 1.02 (0.24), residues: 474 sheet: -0.53 (0.45), residues: 119 loop : -0.60 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 528 HIS 0.003 0.001 HIS A 359 PHE 0.015 0.001 PHE A 990 TYR 0.010 0.001 TYR A1361 ARG 0.004 0.000 ARG A 73 *********************** 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 187 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8383 (mm) cc_final: 0.8175 (mm) REVERT: A 63 LYS cc_start: 0.7171 (tptm) cc_final: 0.6722 (tptm) REVERT: A 64 TYR cc_start: 0.7778 (m-80) cc_final: 0.7522 (m-80) REVERT: A 69 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7432 (ttm170) REVERT: A 79 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7180 (mm-30) REVERT: A 93 GLU cc_start: 0.7544 (tp30) cc_final: 0.7060 (tp30) REVERT: A 107 LYS cc_start: 0.7112 (ttmt) cc_final: 0.6879 (ttmt) REVERT: A 138 GLU cc_start: 0.6017 (mp0) cc_final: 0.5709 (mm-30) REVERT: A 168 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: A 201 PHE cc_start: 0.7235 (t80) cc_final: 0.6873 (t80) REVERT: A 265 PHE cc_start: 0.3807 (m-80) cc_final: 0.3053 (m-80) REVERT: A 280 LYS cc_start: 0.7277 (ttpt) cc_final: 0.6937 (ttmm) REVERT: A 298 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6981 (mm-30) REVERT: A 309 LYS cc_start: 0.7913 (mmmm) cc_final: 0.7697 (mmmm) REVERT: A 317 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6637 (mm-30) REVERT: A 330 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7773 (mm-30) REVERT: A 357 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6594 (mp0) REVERT: A 365 LYS cc_start: 0.7520 (ptpt) cc_final: 0.7228 (ptpp) REVERT: A 367 ASP cc_start: 0.6992 (p0) cc_final: 0.6359 (p0) REVERT: A 374 GLU cc_start: 0.7285 (tp30) cc_final: 0.6954 (mp0) REVERT: A 671 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7742 (mmtp) REVERT: A 991 GLU cc_start: 0.7057 (tp30) cc_final: 0.6580 (mm-30) REVERT: A 1013 LEU cc_start: 0.7879 (tp) cc_final: 0.7594 (tm) REVERT: A 1124 ILE cc_start: 0.7534 (pt) cc_final: 0.7302 (pp) REVERT: A 1133 LYS cc_start: 0.8081 (tttt) cc_final: 0.7725 (ttmt) REVERT: A 1186 LYS cc_start: 0.7455 (mmtm) cc_final: 0.7123 (mmtm) REVERT: A 1221 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6505 (mp0) REVERT: A 1230 ASP cc_start: 0.7011 (t70) cc_final: 0.6741 (m-30) REVERT: A 1238 LYS cc_start: 0.7783 (mtmm) cc_final: 0.7302 (mptt) REVERT: A 1296 GLU cc_start: 0.7810 (tt0) cc_final: 0.7310 (pt0) REVERT: A 1316 LEU cc_start: 0.6845 (pt) cc_final: 0.6613 (mp) REVERT: A 1323 ARG cc_start: 0.6581 (ptt90) cc_final: 0.6074 (ptt90) REVERT: A 1364 GLU cc_start: 0.7201 (tp30) cc_final: 0.6532 (mp0) REVERT: A 1370 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6759 (mm-30) REVERT: A 1388 LYS cc_start: 0.7221 (ttmm) cc_final: 0.6924 (ttmm) outliers start: 19 outliers final: 9 residues processed: 178 average time/residue: 1.4242 time to fit residues: 273.6542 Evaluate side-chains 165 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 168 GLU 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 1180 ILE Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain A residue 1216 LYS 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 117 optimal weight: 0.0060 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 0.0010 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 113 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 overall best weight: 0.3802 ------------------------------------------------------------------------------- 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 A1346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13503 Z= 0.178 Angle : 0.525 12.962 18840 Z= 0.284 Chirality : 0.038 0.192 2114 Planarity : 0.003 0.053 1895 Dihedral : 20.641 120.245 3239 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.54 % Allowed : 12.61 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.24), residues: 1195 helix: 1.07 (0.24), residues: 472 sheet: -0.53 (0.46), residues: 119 loop : -0.61 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 528 HIS 0.004 0.001 HIS A1108 PHE 0.012 0.001 PHE A 990 TYR 0.013 0.001 TYR A 937 ARG 0.005 0.000 ARG A 381 *********************** 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 187 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.7161 (tptm) cc_final: 0.6720 (tptm) REVERT: A 64 TYR cc_start: 0.7655 (m-80) cc_final: 0.7362 (m-80) REVERT: A 69 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7387 (ttm170) REVERT: A 79 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7173 (mm-30) REVERT: A 93 GLU cc_start: 0.7567 (tp30) cc_final: 0.7067 (tp30) REVERT: A 107 LYS cc_start: 0.7072 (ttmt) cc_final: 0.6781 (ttmt) REVERT: A 138 GLU cc_start: 0.6049 (mp0) cc_final: 0.5744 (mm-30) REVERT: A 168 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: A 201 PHE cc_start: 0.7232 (t80) cc_final: 0.6903 (t80) REVERT: A 265 PHE cc_start: 0.3388 (m-80) cc_final: 0.2597 (m-80) REVERT: A 280 LYS cc_start: 0.7283 (ttpt) cc_final: 0.6925 (ttmt) REVERT: A 298 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6980 (mm-30) REVERT: A 309 LYS cc_start: 0.7977 (mmmm) cc_final: 0.7757 (mmmm) REVERT: A 317 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6622 (mm-30) REVERT: A 330 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 357 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6632 (mp0) REVERT: A 367 ASP cc_start: 0.6919 (p0) cc_final: 0.6341 (p0) REVERT: A 374 GLU cc_start: 0.7355 (tp30) cc_final: 0.7004 (mp0) REVERT: A 991 GLU cc_start: 0.7030 (tp30) cc_final: 0.6591 (mm-30) REVERT: A 1013 LEU cc_start: 0.7921 (tp) cc_final: 0.7660 (tm) REVERT: A 1124 ILE cc_start: 0.7529 (pt) cc_final: 0.7301 (pp) REVERT: A 1133 LYS cc_start: 0.8062 (tttt) cc_final: 0.7719 (ttmt) REVERT: A 1186 LYS cc_start: 0.7398 (mmtm) cc_final: 0.7070 (mmtm) REVERT: A 1230 ASP cc_start: 0.6973 (t70) cc_final: 0.6709 (m-30) REVERT: A 1238 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7282 (mptt) REVERT: A 1296 GLU cc_start: 0.7714 (tt0) cc_final: 0.7283 (pt0) REVERT: A 1323 ARG cc_start: 0.6422 (ptt90) cc_final: 0.5887 (ptt90) REVERT: A 1364 GLU cc_start: 0.7085 (tp30) cc_final: 0.6703 (mp0) REVERT: A 1388 LYS cc_start: 0.7138 (ttmm) cc_final: 0.6859 (ttmm) outliers start: 17 outliers final: 6 residues processed: 181 average time/residue: 1.4056 time to fit residues: 274.3433 Evaluate side-chains 167 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1187 SER 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 105 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 108 optimal weight: 0.0870 chunk 87 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13503 Z= 0.181 Angle : 0.509 12.038 18840 Z= 0.278 Chirality : 0.038 0.191 2114 Planarity : 0.003 0.053 1895 Dihedral : 20.623 119.708 3239 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.36 % Allowed : 13.16 % Favored : 84.48 % 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: 0.05 (0.24), residues: 1195 helix: 1.11 (0.24), residues: 472 sheet: -0.80 (0.42), residues: 131 loop : -0.60 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 528 HIS 0.006 0.001 HIS A1033 PHE 0.021 0.001 PHE A1102 TYR 0.023 0.001 TYR A1134 ARG 0.010 0.000 ARG A 381 *********************** 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 192 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.7153 (tptm) cc_final: 0.6713 (tptm) REVERT: A 64 TYR cc_start: 0.7661 (m-80) cc_final: 0.7362 (m-80) REVERT: A 69 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7427 (ttm170) REVERT: A 79 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7171 (mm-30) REVERT: A 93 GLU cc_start: 0.7533 (tp30) cc_final: 0.7004 (tp30) REVERT: A 107 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6766 (ttmt) REVERT: A 138 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5768 (mm-30) REVERT: A 168 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: A 201 PHE cc_start: 0.7194 (t80) cc_final: 0.6836 (t80) REVERT: A 265 PHE cc_start: 0.3542 (m-80) cc_final: 0.2682 (m-80) REVERT: A 280 LYS cc_start: 0.7335 (ttpt) cc_final: 0.6992 (ttmm) REVERT: A 298 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7027 (mm-30) REVERT: A 309 LYS cc_start: 0.7957 (mmmm) cc_final: 0.7726 (mmmm) REVERT: A 317 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6591 (mm-30) REVERT: A 319 LYS cc_start: 0.7642 (ptmm) cc_final: 0.7300 (ptpp) REVERT: A 330 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 357 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 367 ASP cc_start: 0.6836 (p0) cc_final: 0.6288 (p0) REVERT: A 374 GLU cc_start: 0.7340 (tp30) cc_final: 0.7018 (mp0) REVERT: A 991 GLU cc_start: 0.6993 (tp30) cc_final: 0.6570 (mm-30) REVERT: A 1013 LEU cc_start: 0.7942 (tp) cc_final: 0.7693 (tm) REVERT: A 1028 ARG cc_start: 0.6670 (ttp80) cc_final: 0.6394 (ttp-170) REVERT: A 1144 GLU cc_start: 0.7563 (pt0) cc_final: 0.7340 (pt0) REVERT: A 1186 LYS cc_start: 0.7405 (mmtm) cc_final: 0.7071 (mmtm) REVERT: A 1230 ASP cc_start: 0.6961 (t70) cc_final: 0.6731 (m-30) REVERT: A 1238 LYS cc_start: 0.7794 (mtmm) cc_final: 0.7260 (mptt) REVERT: A 1296 GLU cc_start: 0.7671 (tt0) cc_final: 0.7249 (pt0) REVERT: A 1323 ARG cc_start: 0.6474 (ptt90) cc_final: 0.5946 (ptt90) REVERT: A 1364 GLU cc_start: 0.7088 (tp30) cc_final: 0.6752 (mp0) REVERT: A 1388 LYS cc_start: 0.7110 (ttmm) cc_final: 0.6819 (ttmm) REVERT: A 1395 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7193 (mt-10) outliers start: 26 outliers final: 13 residues processed: 179 average time/residue: 1.4331 time to fit residues: 277.2654 Evaluate side-chains 177 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 168 GLU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 74 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13503 Z= 0.226 Angle : 0.534 12.052 18840 Z= 0.291 Chirality : 0.039 0.202 2114 Planarity : 0.004 0.054 1895 Dihedral : 20.602 118.674 3239 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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 (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: 1.00 (0.24), residues: 472 sheet: -0.94 (0.44), residues: 121 loop : -0.60 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 528 HIS 0.007 0.001 HIS A1033 PHE 0.013 0.001 PHE A 990 TYR 0.019 0.001 TYR A1134 ARG 0.008 0.001 ARG A 381 *********************** 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 fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.7169 (tptm) cc_final: 0.6719 (tptm) REVERT: A 64 TYR cc_start: 0.7801 (m-80) cc_final: 0.7512 (m-80) REVERT: A 79 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7188 (mm-30) REVERT: A 93 GLU cc_start: 0.7510 (tp30) cc_final: 0.6881 (tp30) REVERT: A 107 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6781 (ttmt) REVERT: A 138 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5845 (mm-30) REVERT: A 168 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: A 201 PHE cc_start: 0.7210 (t80) cc_final: 0.6815 (t80) REVERT: A 232 TYR cc_start: 0.6183 (t80) cc_final: 0.5978 (m-80) REVERT: A 265 PHE cc_start: 0.3967 (m-80) cc_final: 0.2875 (m-80) REVERT: A 280 LYS cc_start: 0.7342 (ttpt) cc_final: 0.7013 (ttmt) REVERT: A 298 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7020 (mp0) REVERT: A 301 LEU cc_start: 0.8135 (mt) cc_final: 0.7915 (mm) REVERT: A 311 LYS cc_start: 0.7894 (tppt) cc_final: 0.7407 (mmmm) REVERT: A 317 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6604 (mm-30) REVERT: A 330 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 357 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6911 (mm-30) REVERT: A 367 ASP cc_start: 0.6824 (p0) cc_final: 0.6262 (p0) REVERT: A 374 GLU cc_start: 0.7332 (tp30) cc_final: 0.7062 (mp0) REVERT: A 696 ASP cc_start: 0.6545 (m-30) cc_final: 0.6295 (m-30) REVERT: A 1013 LEU cc_start: 0.8064 (tp) cc_final: 0.7820 (tm) REVERT: A 1028 ARG cc_start: 0.6673 (ttp80) cc_final: 0.6233 (ttp80) REVERT: A 1037 ASP cc_start: 0.7209 (m-30) cc_final: 0.6810 (m-30) REVERT: A 1133 LYS cc_start: 0.8045 (tttt) cc_final: 0.7722 (ttmt) REVERT: A 1186 LYS cc_start: 0.7441 (mmtm) cc_final: 0.7100 (mmtm) REVERT: A 1230 ASP cc_start: 0.6968 (t70) cc_final: 0.6753 (m-30) REVERT: A 1238 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7267 (mptt) REVERT: A 1296 GLU cc_start: 0.7668 (tt0) cc_final: 0.7228 (pt0) REVERT: A 1364 GLU cc_start: 0.7095 (tp30) cc_final: 0.6757 (mp0) REVERT: A 1380 TYR cc_start: 0.6772 (m-80) cc_final: 0.6267 (m-80) REVERT: A 1395 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7227 (mm-30) outliers start: 23 outliers final: 13 residues processed: 169 average time/residue: 1.3527 time to fit residues: 247.4364 Evaluate side-chains 181 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 107 LYS Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 168 GLU 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 1103 THR Chi-restraints excluded: chain A residue 1142 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 92 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13503 Z= 0.205 Angle : 0.523 11.993 18840 Z= 0.284 Chirality : 0.039 0.191 2114 Planarity : 0.004 0.053 1895 Dihedral : 20.496 118.088 3239 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.00 % Allowed : 13.79 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.24), residues: 1195 helix: 1.06 (0.24), residues: 474 sheet: -0.68 (0.45), residues: 130 loop : -0.59 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 528 HIS 0.006 0.001 HIS A1033 PHE 0.021 0.001 PHE A1102 TYR 0.015 0.001 TYR A 186 ARG 0.006 0.000 ARG A 381 *********************** 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 183 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.7172 (tptm) cc_final: 0.6716 (tptm) REVERT: A 64 TYR cc_start: 0.7803 (m-80) cc_final: 0.7498 (m-80) REVERT: A 69 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7436 (ttm170) REVERT: A 79 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7131 (mm-30) REVERT: A 93 GLU cc_start: 0.7501 (tp30) cc_final: 0.6878 (tp30) REVERT: A 107 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6848 (ttmm) REVERT: A 138 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5863 (mm-30) REVERT: A 168 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: A 232 TYR cc_start: 0.6237 (t80) cc_final: 0.5837 (m-80) REVERT: A 280 LYS cc_start: 0.7338 (ttpt) cc_final: 0.6960 (ttmt) REVERT: A 298 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7019 (mp0) REVERT: A 311 LYS cc_start: 0.7869 (tppt) cc_final: 0.7393 (mmmm) REVERT: A 317 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6687 (tp30) REVERT: A 319 LYS cc_start: 0.7654 (ptmm) cc_final: 0.7254 (ptpp) REVERT: A 323 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 357 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6946 (mm-30) REVERT: A 367 ASP cc_start: 0.6824 (p0) cc_final: 0.6304 (p0) REVERT: A 374 GLU cc_start: 0.7305 (tp30) cc_final: 0.7072 (mp0) REVERT: A 710 ASN cc_start: 0.7593 (m110) cc_final: 0.7237 (m-40) REVERT: A 995 GLN cc_start: 0.7018 (tp40) cc_final: 0.6414 (mp10) REVERT: A 997 THR cc_start: 0.6649 (OUTLIER) cc_final: 0.6360 (p) REVERT: A 1013 LEU cc_start: 0.8040 (tp) cc_final: 0.7784 (tm) REVERT: A 1037 ASP cc_start: 0.7227 (m-30) cc_final: 0.6844 (m-30) REVERT: A 1186 LYS cc_start: 0.7416 (mmtm) cc_final: 0.7091 (mmtm) REVERT: A 1219 ASN cc_start: 0.7420 (t0) cc_final: 0.7040 (t0) REVERT: A 1222 LEU cc_start: 0.8047 (mp) cc_final: 0.7796 (mt) REVERT: A 1238 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7236 (mptt) REVERT: A 1296 GLU cc_start: 0.7674 (tt0) cc_final: 0.7123 (pt0) REVERT: A 1323 ARG cc_start: 0.6403 (ptt90) cc_final: 0.5868 (ptt90) REVERT: A 1364 GLU cc_start: 0.7109 (tp30) cc_final: 0.6745 (mp0) REVERT: A 1380 TYR cc_start: 0.6750 (m-80) cc_final: 0.6427 (m-80) REVERT: A 1395 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7172 (mm-30) outliers start: 22 outliers final: 15 residues processed: 169 average time/residue: 1.3914 time to fit residues: 254.2445 Evaluate side-chains 174 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1016 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.0670 chunk 62 optimal weight: 0.0470 chunk 11 optimal weight: 0.0370 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 0.0870 overall best weight: 0.2474 ------------------------------------------------------------------------------- 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** A1108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13503 Z= 0.153 Angle : 0.504 11.057 18840 Z= 0.272 Chirality : 0.037 0.186 2114 Planarity : 0.003 0.053 1895 Dihedral : 20.438 117.382 3239 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.63 % Allowed : 14.97 % 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: 0.17 (0.24), residues: 1195 helix: 1.19 (0.24), residues: 471 sheet: -0.53 (0.46), residues: 130 loop : -0.57 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 528 HIS 0.007 0.001 HIS A1033 PHE 0.012 0.001 PHE A 669 TYR 0.013 0.001 TYR A 186 ARG 0.005 0.000 ARG A 381 *********************** 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 180 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.7135 (tptm) cc_final: 0.6677 (tptm) REVERT: A 64 TYR cc_start: 0.7656 (m-80) cc_final: 0.7385 (m-80) REVERT: A 69 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7437 (ttm170) REVERT: A 79 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7165 (mm-30) REVERT: A 93 GLU cc_start: 0.7517 (tp30) cc_final: 0.6993 (tm-30) REVERT: A 107 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6710 (ttmt) REVERT: A 119 LYS cc_start: 0.7662 (tttm) cc_final: 0.7419 (tttm) REVERT: A 138 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5781 (mm-30) REVERT: A 168 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: A 265 PHE cc_start: 0.3945 (m-80) cc_final: 0.2860 (m-80) REVERT: A 279 THR cc_start: 0.7400 (t) cc_final: 0.7174 (t) REVERT: A 280 LYS cc_start: 0.7423 (ttpt) cc_final: 0.7114 (ttmm) REVERT: A 283 GLN cc_start: 0.7373 (tt0) cc_final: 0.7163 (tt0) REVERT: A 298 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7016 (mp0) REVERT: A 309 LYS cc_start: 0.7930 (mmmm) cc_final: 0.7698 (mmmm) REVERT: A 311 LYS cc_start: 0.7896 (tppt) cc_final: 0.7369 (mmmm) REVERT: A 317 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6628 (tp30) REVERT: A 319 LYS cc_start: 0.7631 (ptmm) cc_final: 0.7244 (ptpp) REVERT: A 323 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 357 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6911 (mm-30) REVERT: A 367 ASP cc_start: 0.6721 (p0) cc_final: 0.6242 (p0) REVERT: A 374 GLU cc_start: 0.7308 (tp30) cc_final: 0.7062 (mp0) REVERT: A 710 ASN cc_start: 0.7653 (m110) cc_final: 0.7263 (m-40) REVERT: A 986 ILE cc_start: 0.7631 (pt) cc_final: 0.7184 (pp) REVERT: A 995 GLN cc_start: 0.7015 (tp40) cc_final: 0.6575 (mp10) REVERT: A 997 THR cc_start: 0.6684 (OUTLIER) cc_final: 0.6382 (p) REVERT: A 1013 LEU cc_start: 0.7977 (tp) cc_final: 0.7739 (tm) REVERT: A 1037 ASP cc_start: 0.7175 (m-30) cc_final: 0.6821 (m-30) REVERT: A 1142 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6892 (m-40) REVERT: A 1186 LYS cc_start: 0.7378 (mmtm) cc_final: 0.7038 (mmtm) REVERT: A 1219 ASN cc_start: 0.7410 (t0) cc_final: 0.7041 (t0) REVERT: A 1222 LEU cc_start: 0.8008 (mp) cc_final: 0.7752 (mt) REVERT: A 1238 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7242 (mptt) REVERT: A 1241 ASP cc_start: 0.7424 (m-30) cc_final: 0.7147 (m-30) REVERT: A 1296 GLU cc_start: 0.7654 (tt0) cc_final: 0.7189 (pt0) REVERT: A 1323 ARG cc_start: 0.6443 (ptt90) cc_final: 0.5915 (ptt90) REVERT: A 1380 TYR cc_start: 0.6709 (m-80) cc_final: 0.6366 (m-80) REVERT: A 1395 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7196 (mm-30) outliers start: 18 outliers final: 9 residues processed: 165 average time/residue: 1.4745 time to fit residues: 263.0500 Evaluate side-chains 173 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1142 ASN Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain A residue 1231 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 117 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A1108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.4542 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= 0.267 Angle : 0.560 11.270 18840 Z= 0.304 Chirality : 0.041 0.186 2114 Planarity : 0.004 0.054 1895 Dihedral : 20.544 116.766 3239 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.09 % Allowed : 15.15 % Favored : 82.76 % 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: -0.06 (0.24), residues: 1195 helix: 0.94 (0.24), residues: 474 sheet: -0.76 (0.48), residues: 120 loop : -0.63 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 528 HIS 0.008 0.001 HIS A1033 PHE 0.025 0.001 PHE A1102 TYR 0.016 0.002 TYR A1239 ARG 0.007 0.001 ARG A 381 *********************** 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 176 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.7270 (tptm) cc_final: 0.6768 (tptm) REVERT: A 64 TYR cc_start: 0.7813 (m-80) cc_final: 0.7589 (m-80) REVERT: A 79 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7277 (mp0) REVERT: A 93 GLU cc_start: 0.7491 (tp30) cc_final: 0.6906 (tp30) REVERT: A 119 LYS cc_start: 0.7606 (tttm) cc_final: 0.7370 (tttm) REVERT: A 138 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5995 (mm-30) REVERT: A 168 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 232 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.5994 (m-10) REVERT: A 279 THR cc_start: 0.7549 (t) cc_final: 0.7296 (t) REVERT: A 280 LYS cc_start: 0.7308 (ttpt) cc_final: 0.6960 (ttmm) REVERT: A 283 GLN cc_start: 0.7355 (tt0) cc_final: 0.7152 (tt0) REVERT: A 298 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7019 (mp0) REVERT: A 309 LYS cc_start: 0.8001 (mmmm) cc_final: 0.7773 (mmmm) REVERT: A 311 LYS cc_start: 0.7918 (tppt) cc_final: 0.7379 (mmmm) REVERT: A 317 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6631 (tp30) REVERT: A 319 LYS cc_start: 0.7635 (ptmm) cc_final: 0.7259 (ptpp) REVERT: A 323 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 330 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7783 (mt-10) REVERT: A 357 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6838 (mm-30) REVERT: A 367 ASP cc_start: 0.6849 (p0) cc_final: 0.6298 (p0) REVERT: A 374 GLU cc_start: 0.7295 (tp30) cc_final: 0.7071 (mp0) REVERT: A 995 GLN cc_start: 0.6994 (tp40) cc_final: 0.6594 (mp10) REVERT: A 997 THR cc_start: 0.6697 (OUTLIER) cc_final: 0.6449 (p) REVERT: A 1013 LEU cc_start: 0.8041 (tp) cc_final: 0.7786 (tm) REVERT: A 1028 ARG cc_start: 0.6683 (ttp80) cc_final: 0.6271 (ttp80) REVERT: A 1037 ASP cc_start: 0.7319 (m-30) cc_final: 0.6889 (m-30) REVERT: A 1133 LYS cc_start: 0.8076 (tttt) cc_final: 0.7750 (ttmt) REVERT: A 1142 ASN cc_start: 0.7243 (OUTLIER) cc_final: 0.6940 (m-40) REVERT: A 1167 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7857 (tttp) REVERT: A 1186 LYS cc_start: 0.7450 (mmtm) cc_final: 0.7112 (mmtm) REVERT: A 1219 ASN cc_start: 0.7555 (t0) cc_final: 0.7182 (t0) REVERT: A 1222 LEU cc_start: 0.8042 (mp) cc_final: 0.7797 (mt) REVERT: A 1238 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7245 (mptt) REVERT: A 1296 GLU cc_start: 0.7672 (tt0) cc_final: 0.7190 (pt0) REVERT: A 1323 ARG cc_start: 0.6398 (ptt90) cc_final: 0.5901 (ptt90) REVERT: A 1364 GLU cc_start: 0.7117 (tp30) cc_final: 0.6770 (mp0) REVERT: A 1380 TYR cc_start: 0.6841 (m-80) cc_final: 0.6395 (m-80) REVERT: A 1395 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7163 (mm-30) outliers start: 23 outliers final: 13 residues processed: 160 average time/residue: 1.4371 time to fit residues: 248.2693 Evaluate side-chains 171 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 138 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1142 ASN Chi-restraints excluded: chain A residue 1167 LYS 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 75 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13503 Z= 0.290 Angle : 0.578 11.614 18840 Z= 0.309 Chirality : 0.041 0.185 2114 Planarity : 0.004 0.054 1895 Dihedral : 20.557 116.077 3239 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.72 % Allowed : 15.52 % Favored : 82.76 % 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: -0.19 (0.24), residues: 1195 helix: 0.85 (0.24), residues: 473 sheet: -0.91 (0.48), residues: 120 loop : -0.70 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 528 HIS 0.017 0.001 HIS A 336 PHE 0.017 0.002 PHE A 669 TYR 0.017 0.002 TYR A 186 ARG 0.007 0.001 ARG A 381 ********************** 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 171 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7524 (p) REVERT: A 63 LYS cc_start: 0.7252 (tptm) cc_final: 0.6750 (tptm) REVERT: A 64 TYR cc_start: 0.7862 (m-80) cc_final: 0.7611 (m-80) REVERT: A 79 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 93 GLU cc_start: 0.7480 (tp30) cc_final: 0.6958 (tm-30) REVERT: A 119 LYS cc_start: 0.7590 (tttm) cc_final: 0.7352 (tttm) REVERT: A 138 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.6063 (mm-30) REVERT: A 168 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: A 232 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.5869 (m-10) REVERT: A 242 TRP cc_start: 0.6554 (m100) cc_final: 0.6288 (m100) REVERT: A 279 THR cc_start: 0.7558 (t) cc_final: 0.7310 (t) REVERT: A 280 LYS cc_start: 0.7305 (ttpt) cc_final: 0.7001 (ttmt) REVERT: A 298 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6988 (mp0) REVERT: A 309 LYS cc_start: 0.7947 (mmmm) cc_final: 0.7715 (mmmm) REVERT: A 311 LYS cc_start: 0.7881 (tppt) cc_final: 0.7410 (mmmm) REVERT: A 317 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6603 (tp30) REVERT: A 319 LYS cc_start: 0.7636 (ptmm) cc_final: 0.7263 (ptpp) REVERT: A 323 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 357 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6827 (mm-30) REVERT: A 367 ASP cc_start: 0.6873 (p0) cc_final: 0.6311 (p0) REVERT: A 374 GLU cc_start: 0.7310 (tp30) cc_final: 0.7070 (mp0) REVERT: A 995 GLN cc_start: 0.7063 (tp40) cc_final: 0.6636 (mp10) REVERT: A 997 THR cc_start: 0.6728 (OUTLIER) cc_final: 0.6444 (p) REVERT: A 1013 LEU cc_start: 0.8024 (tp) cc_final: 0.7751 (tm) REVERT: A 1028 ARG cc_start: 0.6694 (ttp80) cc_final: 0.6189 (ttp80) REVERT: A 1037 ASP cc_start: 0.7322 (m-30) cc_final: 0.6945 (m-30) REVERT: A 1142 ASN cc_start: 0.7330 (OUTLIER) cc_final: 0.7032 (m-40) REVERT: A 1186 LYS cc_start: 0.7450 (mmtm) cc_final: 0.7115 (mmtm) REVERT: A 1219 ASN cc_start: 0.7563 (t0) cc_final: 0.7190 (t0) REVERT: A 1222 LEU cc_start: 0.8059 (mp) cc_final: 0.7814 (mt) REVERT: A 1238 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7253 (mptt) REVERT: A 1296 GLU cc_start: 0.7709 (tt0) cc_final: 0.7154 (pt0) REVERT: A 1323 ARG cc_start: 0.6373 (ptt90) cc_final: 0.5907 (ptt90) REVERT: A 1364 GLU cc_start: 0.7104 (tp30) cc_final: 0.6783 (mp0) REVERT: A 1380 TYR cc_start: 0.6835 (m-80) cc_final: 0.6312 (m-80) REVERT: A 1395 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7162 (mm-30) outliers start: 19 outliers final: 11 residues processed: 159 average time/residue: 1.4895 time to fit residues: 255.0652 Evaluate side-chains 167 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 138 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1142 ASN Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain A residue 1229 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 31 optimal weight: 0.3980 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4690 r_free = 0.4690 target = 0.228237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.168239 restraints weight = 42358.604| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.81 r_work: 0.3768 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 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 = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13503 Z= 0.231 Angle : 0.549 11.688 18840 Z= 0.295 Chirality : 0.040 0.184 2114 Planarity : 0.004 0.054 1895 Dihedral : 20.533 115.108 3239 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.81 % Allowed : 15.70 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.24), residues: 1195 helix: 0.82 (0.24), residues: 477 sheet: -0.85 (0.49), residues: 115 loop : -0.69 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 528 HIS 0.007 0.001 HIS A1033 PHE 0.026 0.001 PHE A1102 TYR 0.014 0.001 TYR A1239 ARG 0.007 0.000 ARG A 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5256.14 seconds wall clock time: 92 minutes 25.81 seconds (5545.81 seconds total)