Starting phenix.real_space_refine on Sun Jul 21 02:25:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/07_2024/8wmh_37652.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/07_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_37652/07_2024/8wmh_37652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/07_2024/8wmh_37652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/07_2024/8wmh_37652.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmh_37652/07_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-5388/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: 12.04, per 1000 atoms: 0.93 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: 5.89 Conformation dependent library (CDL) restraints added in 3.7 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: 4.98 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: 7.04 Time building geometry restraints manager: 6.40 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 2.440 nonbonded pdb=" O LYS A 109 " pdb=" OG1 THR A 112 " model vdw 2.221 2.440 nonbonded pdb=" OG SER A 385 " pdb=" OP1 C O 118 " model vdw 2.230 2.440 nonbonded pdb=" OE1 GLU A1132 " pdb=" O2' U O 86 " model vdw 2.235 2.440 nonbonded pdb=" O2' G O 107 " pdb=" OP1 C O 108 " model vdw 2.247 2.440 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 49.950 Find NCS groups from input model: 0.130 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: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.390 ------------------------------------------------------------------------------- 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 : 1.182 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: 1.3336 time to fit residues: 258.9036 Evaluate side-chains 155 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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: 0.4980 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 50.0000 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 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 98 GLN A 287 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13503 Z= 0.272 Angle : 0.609 13.515 18840 Z= 0.326 Chirality : 0.042 0.168 2114 Planarity : 0.004 0.049 1895 Dihedral : 20.867 121.227 3245 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.36 % Allowed : 8.71 % Favored : 89.93 % 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: -0.12 (0.24), residues: 1195 helix: 0.80 (0.23), residues: 472 sheet: -0.50 (0.41), residues: 146 loop : -0.64 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1005 HIS 0.006 0.001 HIS A1160 PHE 0.016 0.002 PHE A 990 TYR 0.015 0.002 TYR A1286 ARG 0.005 0.001 ARG A 989 *********************** 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 186 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8386 (mm) cc_final: 0.8154 (mm) REVERT: A 63 LYS cc_start: 0.7259 (tptm) cc_final: 0.6801 (tptm) REVERT: A 64 TYR cc_start: 0.7751 (m-80) cc_final: 0.7417 (m-80) REVERT: A 79 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7247 (mm-30) REVERT: A 93 GLU cc_start: 0.7477 (tp30) cc_final: 0.7014 (tp30) REVERT: A 119 LYS cc_start: 0.7728 (tttm) cc_final: 0.7405 (tttm) REVERT: A 138 GLU cc_start: 0.5968 (mp0) cc_final: 0.5693 (mm-30) REVERT: A 164 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7855 (p) REVERT: A 168 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: A 201 PHE cc_start: 0.7307 (t80) cc_final: 0.6963 (t80) REVERT: A 265 PHE cc_start: 0.3758 (m-80) cc_final: 0.3100 (m-80) REVERT: A 280 LYS cc_start: 0.7302 (ttpt) cc_final: 0.6955 (ttmm) REVERT: A 286 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: A 298 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7056 (mt-10) REVERT: A 311 LYS cc_start: 0.7905 (tppt) cc_final: 0.7521 (tppt) REVERT: A 317 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6409 (mm-30) REVERT: A 326 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7183 (ttm-80) REVERT: A 330 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7723 (mm-30) REVERT: A 357 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6690 (mp0) REVERT: A 365 LYS cc_start: 0.7457 (ptpt) cc_final: 0.7194 (ptpp) REVERT: A 374 GLU cc_start: 0.7117 (tp30) cc_final: 0.6861 (mp0) REVERT: A 381 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7399 (mtt90) REVERT: A 671 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7800 (mmtm) REVERT: A 980 ASP cc_start: 0.6908 (t0) cc_final: 0.6508 (t0) REVERT: A 991 GLU cc_start: 0.7080 (tp30) cc_final: 0.6507 (mm-30) REVERT: A 1000 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7635 (mmpt) REVERT: A 1013 LEU cc_start: 0.7903 (tp) cc_final: 0.7672 (tm) REVERT: A 1119 GLN cc_start: 0.7805 (mt0) cc_final: 0.7519 (mm-40) REVERT: A 1124 ILE cc_start: 0.7607 (pt) cc_final: 0.7355 (pp) REVERT: A 1156 ARG cc_start: 0.7815 (mmm-85) cc_final: 0.7601 (mmm-85) REVERT: A 1177 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7485 (ttpp) REVERT: A 1186 LYS cc_start: 0.7449 (mmtm) cc_final: 0.7135 (mmtm) REVERT: A 1221 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6435 (mp0) REVERT: A 1238 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7323 (mptt) REVERT: A 1243 LYS cc_start: 0.7208 (mttp) cc_final: 0.6914 (mtpp) REVERT: A 1296 GLU cc_start: 0.7957 (tt0) cc_final: 0.7159 (pt0) REVERT: A 1323 ARG cc_start: 0.6598 (ptt90) cc_final: 0.6114 (ptt90) REVERT: A 1332 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6880 (p0) REVERT: A 1380 TYR cc_start: 0.6793 (m-10) cc_final: 0.6408 (m-80) REVERT: A 1389 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7168 (p) REVERT: A 1408 ARG cc_start: 0.7038 (ttm170) cc_final: 0.6821 (ttt180) outliers start: 15 outliers final: 3 residues processed: 179 average time/residue: 1.4625 time to fit residues: 282.8698 Evaluate side-chains 163 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 286 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1389 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 40 optimal weight: 30.0000 chunk 95 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13503 Z= 0.259 Angle : 0.556 13.698 18840 Z= 0.300 Chirality : 0.040 0.166 2114 Planarity : 0.004 0.048 1895 Dihedral : 20.852 121.377 3239 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.54 % Allowed : 11.43 % Favored : 87.02 % 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: 0.82 (0.24), residues: 468 sheet: -0.85 (0.43), residues: 129 loop : -0.63 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 528 HIS 0.003 0.001 HIS A1034 PHE 0.015 0.002 PHE A 990 TYR 0.015 0.002 TYR A1286 ARG 0.007 0.001 ARG A 350 *********************** 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 188 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.7266 (tptm) cc_final: 0.6770 (tptm) REVERT: A 64 TYR cc_start: 0.7808 (m-80) cc_final: 0.7505 (m-80) REVERT: A 79 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7234 (mm-30) REVERT: A 93 GLU cc_start: 0.7450 (tp30) cc_final: 0.6987 (tp30) REVERT: A 107 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6828 (ttmt) REVERT: A 138 GLU cc_start: 0.6162 (mp0) cc_final: 0.5878 (mm-30) REVERT: A 164 SER cc_start: 0.8172 (m) cc_final: 0.7937 (p) REVERT: A 168 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: A 201 PHE cc_start: 0.7325 (t80) cc_final: 0.6840 (t80) REVERT: A 265 PHE cc_start: 0.3480 (m-80) cc_final: 0.2645 (m-80) REVERT: A 280 LYS cc_start: 0.7341 (ttpt) cc_final: 0.7038 (ttmt) REVERT: A 298 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6975 (mm-30) REVERT: A 311 LYS cc_start: 0.7946 (tppt) cc_final: 0.7333 (mmmm) REVERT: A 317 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6603 (tp30) REVERT: A 330 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 357 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6694 (mp0) REVERT: A 365 LYS cc_start: 0.7552 (ptpt) cc_final: 0.7257 (ptpp) REVERT: A 367 ASP cc_start: 0.7074 (p0) cc_final: 0.6377 (p0) REVERT: A 374 GLU cc_start: 0.7344 (tp30) cc_final: 0.7040 (mp0) REVERT: A 660 TRP cc_start: 0.6500 (m-10) cc_final: 0.6241 (m-10) REVERT: A 700 LYS cc_start: 0.6886 (mmtp) cc_final: 0.6589 (mmtt) REVERT: A 980 ASP cc_start: 0.6508 (t0) cc_final: 0.6261 (t0) REVERT: A 991 GLU cc_start: 0.7040 (tp30) cc_final: 0.6376 (mm-30) REVERT: A 995 GLN cc_start: 0.6999 (tp40) cc_final: 0.6602 (mp10) REVERT: A 1000 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7712 (mmpt) REVERT: A 1013 LEU cc_start: 0.7978 (tp) cc_final: 0.7727 (tm) REVERT: A 1033 HIS cc_start: 0.7306 (p-80) cc_final: 0.7097 (p-80) REVERT: A 1037 ASP cc_start: 0.7178 (m-30) cc_final: 0.6907 (m-30) REVERT: A 1119 GLN cc_start: 0.7820 (mt0) cc_final: 0.7457 (mm110) REVERT: A 1124 ILE cc_start: 0.7582 (pt) cc_final: 0.7355 (pp) REVERT: A 1133 LYS cc_start: 0.8104 (tttt) cc_final: 0.7790 (ttmt) REVERT: A 1145 ARG cc_start: 0.7076 (ttm110) cc_final: 0.6863 (mtp-110) REVERT: A 1167 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7893 (tttp) REVERT: A 1186 LYS cc_start: 0.7429 (mmtm) cc_final: 0.7134 (mmtm) REVERT: A 1221 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6505 (mp0) REVERT: A 1238 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7304 (mptt) REVERT: A 1243 LYS cc_start: 0.7251 (mttp) cc_final: 0.7049 (mmtm) REVERT: A 1296 GLU cc_start: 0.7836 (tt0) cc_final: 0.7375 (pt0) REVERT: A 1323 ARG cc_start: 0.6495 (ptt90) cc_final: 0.5959 (ptt90) REVERT: A 1364 GLU cc_start: 0.7120 (tp30) cc_final: 0.6575 (mp0) REVERT: A 1380 TYR cc_start: 0.6920 (m-10) cc_final: 0.6475 (m-80) REVERT: A 1388 LYS cc_start: 0.7201 (ttmm) cc_final: 0.6916 (ttmm) outliers start: 17 outliers final: 8 residues processed: 177 average time/residue: 1.3943 time to fit residues: 266.6177 Evaluate side-chains 174 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 945 ILE 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 1187 SER Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 0.0270 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN A 529 HIS A1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.3386 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= 0.234 Angle : 0.533 13.222 18840 Z= 0.293 Chirality : 0.040 0.181 2114 Planarity : 0.004 0.056 1895 Dihedral : 20.800 119.944 3239 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.18 % Allowed : 12.34 % Favored : 85.48 % 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: -0.21 (0.24), residues: 1195 helix: 0.78 (0.24), residues: 466 sheet: -0.83 (0.43), residues: 129 loop : -0.66 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP A 528 HIS 0.003 0.001 HIS A 157 PHE 0.015 0.001 PHE A 990 TYR 0.013 0.001 TYR A 295 ARG 0.005 0.001 ARG A 350 *********************** 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 197 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 14 SER cc_start: 0.8086 (p) cc_final: 0.7880 (m) REVERT: A 63 LYS cc_start: 0.7247 (tptm) cc_final: 0.6750 (tptm) REVERT: A 64 TYR cc_start: 0.7800 (m-80) cc_final: 0.7525 (m-80) REVERT: A 79 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7213 (mm-30) REVERT: A 93 GLU cc_start: 0.7503 (tp30) cc_final: 0.7011 (tp30) REVERT: A 119 LYS cc_start: 0.7726 (tttm) cc_final: 0.7421 (tttm) REVERT: A 138 GLU cc_start: 0.6177 (mp0) cc_final: 0.5910 (mm-30) REVERT: A 164 SER cc_start: 0.8161 (m) cc_final: 0.7929 (p) REVERT: A 168 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: A 201 PHE cc_start: 0.7336 (t80) cc_final: 0.6811 (t80) REVERT: A 265 PHE cc_start: 0.3869 (m-80) cc_final: 0.2900 (m-80) REVERT: A 280 LYS cc_start: 0.7297 (ttpt) cc_final: 0.6979 (ttmm) REVERT: A 298 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7042 (mm-30) REVERT: A 311 LYS cc_start: 0.7936 (tppt) cc_final: 0.7545 (tppt) REVERT: A 317 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6579 (tp30) REVERT: A 330 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 350 ARG cc_start: 0.6817 (mtm-85) cc_final: 0.6616 (mtm-85) REVERT: A 357 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6677 (mp0) REVERT: A 367 ASP cc_start: 0.7059 (p0) cc_final: 0.6470 (p0) REVERT: A 374 GLU cc_start: 0.7348 (tp30) cc_final: 0.7084 (mp0) REVERT: A 991 GLU cc_start: 0.7061 (tp30) cc_final: 0.6426 (mp0) REVERT: A 995 GLN cc_start: 0.7109 (tp40) cc_final: 0.6653 (mp10) REVERT: A 1013 LEU cc_start: 0.8036 (tp) cc_final: 0.7783 (tm) REVERT: A 1119 GLN cc_start: 0.7890 (mt0) cc_final: 0.7492 (mm110) REVERT: A 1124 ILE cc_start: 0.7448 (pt) cc_final: 0.7243 (pp) REVERT: A 1133 LYS cc_start: 0.8118 (tttt) cc_final: 0.7771 (ttmt) REVERT: A 1145 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6905 (mtp-110) REVERT: A 1167 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7894 (tttp) REVERT: A 1186 LYS cc_start: 0.7409 (mmtm) cc_final: 0.7125 (mmtm) REVERT: A 1221 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6521 (mp0) REVERT: A 1238 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7285 (mptt) REVERT: A 1296 GLU cc_start: 0.7789 (tt0) cc_final: 0.7349 (pt0) REVERT: A 1323 ARG cc_start: 0.6499 (ptt90) cc_final: 0.5962 (ptt90) REVERT: A 1364 GLU cc_start: 0.7083 (tp30) cc_final: 0.6687 (mt-10) REVERT: A 1380 TYR cc_start: 0.6873 (m-10) cc_final: 0.6457 (m-80) REVERT: A 1408 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7315 (ttm-80) outliers start: 24 outliers final: 9 residues processed: 186 average time/residue: 1.3151 time to fit residues: 265.5588 Evaluate side-chains 172 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1167 LYS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain A residue 1301 ASN 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=3.50 ------------------------------------------------------------------------------- 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: 0.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 0.0570 chunk 87 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 529 HIS A 685 GLN A 960 ASN A1346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13503 Z= 0.200 Angle : 0.518 13.072 18840 Z= 0.283 Chirality : 0.039 0.183 2114 Planarity : 0.003 0.045 1895 Dihedral : 20.753 119.721 3239 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.36 % Allowed : 12.89 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.24), residues: 464 sheet: -1.08 (0.42), residues: 136 loop : -0.61 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 528 HIS 0.009 0.001 HIS A1033 PHE 0.014 0.001 PHE A 990 TYR 0.013 0.001 TYR A1239 ARG 0.005 0.000 ARG A 350 *********************** 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 194 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 SER cc_start: 0.7986 (p) cc_final: 0.7783 (m) REVERT: A 63 LYS cc_start: 0.7235 (tptm) cc_final: 0.6741 (tptm) REVERT: A 64 TYR cc_start: 0.7801 (m-80) cc_final: 0.7547 (m-80) REVERT: A 79 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7271 (mm-30) REVERT: A 93 GLU cc_start: 0.7502 (tp30) cc_final: 0.6947 (tp30) REVERT: A 119 LYS cc_start: 0.7718 (tttm) cc_final: 0.7414 (tttm) REVERT: A 138 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5950 (mm-30) REVERT: A 164 SER cc_start: 0.8152 (m) cc_final: 0.7924 (p) REVERT: A 168 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: A 201 PHE cc_start: 0.7285 (t80) cc_final: 0.6809 (t80) REVERT: A 232 TYR cc_start: 0.6219 (t80) cc_final: 0.5819 (m-80) REVERT: A 265 PHE cc_start: 0.3920 (m-80) cc_final: 0.2866 (m-80) REVERT: A 280 LYS cc_start: 0.7294 (ttpt) cc_final: 0.6905 (ttmt) REVERT: A 298 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6895 (mp0) REVERT: A 301 LEU cc_start: 0.8069 (mt) cc_final: 0.7851 (mm) REVERT: A 311 LYS cc_start: 0.7884 (tppt) cc_final: 0.7498 (tppt) REVERT: A 317 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6576 (tp30) REVERT: A 330 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 350 ARG cc_start: 0.6813 (mtm-85) cc_final: 0.6610 (mtm-85) REVERT: A 357 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6879 (mm-30) REVERT: A 367 ASP cc_start: 0.7010 (p0) cc_final: 0.6369 (p0) REVERT: A 374 GLU cc_start: 0.7329 (tp30) cc_final: 0.7073 (mp0) REVERT: A 700 LYS cc_start: 0.7086 (mmtp) cc_final: 0.6822 (mmtt) REVERT: A 710 ASN cc_start: 0.7762 (m110) cc_final: 0.7338 (m-40) REVERT: A 991 GLU cc_start: 0.7035 (tp30) cc_final: 0.6479 (mp0) REVERT: A 995 GLN cc_start: 0.6938 (tp40) cc_final: 0.6593 (mp10) REVERT: A 1013 LEU cc_start: 0.8002 (tp) cc_final: 0.7756 (tm) REVERT: A 1037 ASP cc_start: 0.7118 (m-30) cc_final: 0.6820 (m-30) REVERT: A 1119 GLN cc_start: 0.7894 (mt0) cc_final: 0.7475 (mm110) REVERT: A 1124 ILE cc_start: 0.7506 (pt) cc_final: 0.7224 (pp) REVERT: A 1133 LYS cc_start: 0.8073 (tttt) cc_final: 0.7723 (ttmt) REVERT: A 1167 LYS cc_start: 0.8142 (tttm) cc_final: 0.7877 (tttp) REVERT: A 1186 LYS cc_start: 0.7400 (mmtm) cc_final: 0.7109 (mmtm) REVERT: A 1219 ASN cc_start: 0.7456 (t0) cc_final: 0.7053 (t0) REVERT: A 1221 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6521 (mp0) REVERT: A 1238 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7272 (mptt) REVERT: A 1296 GLU cc_start: 0.7791 (tt0) cc_final: 0.7386 (pt0) REVERT: A 1323 ARG cc_start: 0.6515 (ptt90) cc_final: 0.5991 (ptt90) REVERT: A 1364 GLU cc_start: 0.7113 (tp30) cc_final: 0.6610 (mp0) REVERT: A 1380 TYR cc_start: 0.6812 (m-10) cc_final: 0.6440 (m-80) outliers start: 26 outliers final: 9 residues processed: 177 average time/residue: 1.3760 time to fit residues: 264.3227 Evaluate side-chains 177 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 104 ARG 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 981 VAL 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 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: 6.9990 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13503 Z= 0.293 Angle : 0.573 13.352 18840 Z= 0.311 Chirality : 0.042 0.214 2114 Planarity : 0.004 0.048 1895 Dihedral : 20.701 118.783 3239 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.91 % Allowed : 13.79 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.24), residues: 465 sheet: -0.98 (0.47), residues: 114 loop : -0.69 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 528 HIS 0.008 0.001 HIS A1033 PHE 0.017 0.001 PHE A1102 TYR 0.015 0.002 TYR A 95 ARG 0.006 0.001 ARG A 69 *********************** 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 186 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 SER cc_start: 0.8061 (p) cc_final: 0.7848 (p) REVERT: A 63 LYS cc_start: 0.7245 (tptm) cc_final: 0.6708 (tptm) REVERT: A 64 TYR cc_start: 0.7878 (m-80) cc_final: 0.7621 (m-80) REVERT: A 79 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7332 (mm-30) REVERT: A 93 GLU cc_start: 0.7470 (tp30) cc_final: 0.6922 (tm-30) REVERT: A 119 LYS cc_start: 0.7619 (tttm) cc_final: 0.7328 (tttm) REVERT: A 164 SER cc_start: 0.8144 (m) cc_final: 0.7904 (p) REVERT: A 168 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: A 201 PHE cc_start: 0.7344 (t80) cc_final: 0.6825 (t80) REVERT: A 232 TYR cc_start: 0.6278 (t80) cc_final: 0.5810 (m-80) REVERT: A 280 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6996 (ttmt) REVERT: A 298 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6942 (mp0) REVERT: A 311 LYS cc_start: 0.7896 (tppt) cc_final: 0.7514 (tppt) REVERT: A 317 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6568 (tp30) REVERT: A 357 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6830 (mm-30) REVERT: A 367 ASP cc_start: 0.7117 (p0) cc_final: 0.6526 (p0) REVERT: A 696 ASP cc_start: 0.7001 (m-30) cc_final: 0.6564 (m-30) REVERT: A 710 ASN cc_start: 0.7814 (m110) cc_final: 0.7424 (m-40) REVERT: A 995 GLN cc_start: 0.6977 (tp40) cc_final: 0.6663 (mp10) REVERT: A 1013 LEU cc_start: 0.8121 (tp) cc_final: 0.7828 (tm) REVERT: A 1028 ARG cc_start: 0.6608 (ttp-170) cc_final: 0.6040 (ttp-110) REVERT: A 1037 ASP cc_start: 0.7197 (m-30) cc_final: 0.6786 (m-30) REVERT: A 1119 GLN cc_start: 0.7906 (mt0) cc_final: 0.7474 (mm110) REVERT: A 1124 ILE cc_start: 0.7493 (pt) cc_final: 0.7263 (pp) REVERT: A 1132 GLU cc_start: 0.7355 (mp0) cc_final: 0.5962 (mp0) REVERT: A 1133 LYS cc_start: 0.8084 (tttt) cc_final: 0.7768 (ttmt) REVERT: A 1142 ASN cc_start: 0.7359 (t0) cc_final: 0.7067 (m-40) REVERT: A 1145 ARG cc_start: 0.7297 (mtp-110) cc_final: 0.7069 (mtt-85) REVERT: A 1186 LYS cc_start: 0.7433 (mmtm) cc_final: 0.7152 (mmtm) REVERT: A 1219 ASN cc_start: 0.7475 (t0) cc_final: 0.7094 (t0) REVERT: A 1222 LEU cc_start: 0.8031 (mp) cc_final: 0.7804 (mt) REVERT: A 1238 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7290 (mptt) REVERT: A 1282 PHE cc_start: 0.7889 (m-80) cc_final: 0.7654 (m-80) REVERT: A 1294 SER cc_start: 0.6472 (m) cc_final: 0.6239 (t) REVERT: A 1296 GLU cc_start: 0.7829 (tt0) cc_final: 0.7069 (pt0) REVERT: A 1323 ARG cc_start: 0.6490 (ptt90) cc_final: 0.5970 (ptt90) REVERT: A 1332 ASP cc_start: 0.7242 (p0) cc_final: 0.6824 (p0) REVERT: A 1364 GLU cc_start: 0.7137 (tp30) cc_final: 0.6610 (mp0) REVERT: A 1380 TYR cc_start: 0.6879 (m-10) cc_final: 0.6473 (m-80) outliers start: 21 outliers final: 12 residues processed: 175 average time/residue: 1.3974 time to fit residues: 264.6627 Evaluate side-chains 176 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1016 VAL 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 1301 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 126 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 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 283 GLN A1108 HIS A1301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.4304 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= 0.222 Angle : 0.521 12.661 18840 Z= 0.285 Chirality : 0.039 0.165 2114 Planarity : 0.004 0.048 1895 Dihedral : 20.651 118.433 3239 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.72 % Allowed : 14.61 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.24), residues: 1195 helix: 0.88 (0.24), residues: 468 sheet: -0.78 (0.47), residues: 121 loop : -0.69 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 528 HIS 0.007 0.001 HIS A1033 PHE 0.014 0.001 PHE A 990 TYR 0.013 0.001 TYR A1239 ARG 0.005 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 SER cc_start: 0.8056 (p) cc_final: 0.7831 (p) REVERT: A 63 LYS cc_start: 0.7232 (tptm) cc_final: 0.6711 (tptm) REVERT: A 64 TYR cc_start: 0.7867 (m-80) cc_final: 0.7628 (m-80) REVERT: A 79 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7317 (mm-30) REVERT: A 93 GLU cc_start: 0.7489 (tp30) cc_final: 0.6842 (tm-30) REVERT: A 119 LYS cc_start: 0.7630 (tttm) cc_final: 0.7344 (tttm) REVERT: A 168 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: A 201 PHE cc_start: 0.7294 (t80) cc_final: 0.6800 (t80) REVERT: A 232 TYR cc_start: 0.6242 (t80) cc_final: 0.5868 (m-80) REVERT: A 280 LYS cc_start: 0.7303 (ttpt) cc_final: 0.7001 (ttmt) REVERT: A 298 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6999 (mp0) REVERT: A 301 LEU cc_start: 0.8098 (mt) cc_final: 0.7882 (mm) REVERT: A 311 LYS cc_start: 0.7877 (tppt) cc_final: 0.7501 (tppt) REVERT: A 317 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6575 (tp30) REVERT: A 330 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7828 (mt-10) REVERT: A 357 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6805 (mm-30) REVERT: A 367 ASP cc_start: 0.7026 (p0) cc_final: 0.6446 (p0) REVERT: A 696 ASP cc_start: 0.6760 (m-30) cc_final: 0.6402 (m-30) REVERT: A 710 ASN cc_start: 0.7812 (m110) cc_final: 0.7345 (m-40) REVERT: A 995 GLN cc_start: 0.6993 (tp40) cc_final: 0.6577 (mp10) REVERT: A 1013 LEU cc_start: 0.8060 (tp) cc_final: 0.7779 (tm) REVERT: A 1037 ASP cc_start: 0.7152 (m-30) cc_final: 0.6740 (m-30) REVERT: A 1119 GLN cc_start: 0.7893 (mt0) cc_final: 0.7464 (mm110) REVERT: A 1124 ILE cc_start: 0.7536 (pt) cc_final: 0.7276 (pp) REVERT: A 1132 GLU cc_start: 0.7282 (mp0) cc_final: 0.6026 (mp0) REVERT: A 1145 ARG cc_start: 0.7185 (mtp-110) cc_final: 0.6838 (mtt-85) REVERT: A 1167 LYS cc_start: 0.8098 (tttm) cc_final: 0.7808 (tttp) REVERT: A 1186 LYS cc_start: 0.7408 (mmtm) cc_final: 0.7134 (mmtm) REVERT: A 1219 ASN cc_start: 0.7474 (t0) cc_final: 0.7084 (t0) REVERT: A 1238 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7280 (mptt) REVERT: A 1282 PHE cc_start: 0.7875 (m-80) cc_final: 0.7612 (m-80) REVERT: A 1294 SER cc_start: 0.6527 (m) cc_final: 0.6277 (t) REVERT: A 1296 GLU cc_start: 0.7789 (tt0) cc_final: 0.7336 (pt0) REVERT: A 1323 ARG cc_start: 0.6531 (ptt90) cc_final: 0.5962 (ptt90) REVERT: A 1364 GLU cc_start: 0.7121 (tp30) cc_final: 0.6654 (mp0) REVERT: A 1380 TYR cc_start: 0.6790 (m-10) cc_final: 0.6424 (m-80) outliers start: 19 outliers final: 12 residues processed: 178 average time/residue: 1.3028 time to fit residues: 252.1008 Evaluate side-chains 178 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1301 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 62 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13503 Z= 0.238 Angle : 0.537 12.852 18840 Z= 0.292 Chirality : 0.040 0.165 2114 Planarity : 0.004 0.049 1895 Dihedral : 20.654 117.947 3239 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.91 % Allowed : 15.06 % Favored : 83.03 % 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: 0.90 (0.24), residues: 467 sheet: -0.74 (0.48), residues: 118 loop : -0.73 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 528 HIS 0.007 0.001 HIS A1033 PHE 0.015 0.001 PHE A 990 TYR 0.014 0.001 TYR A 186 ARG 0.005 0.000 ARG A 989 *********************** 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 189 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 SER cc_start: 0.8052 (p) cc_final: 0.7807 (p) REVERT: A 63 LYS cc_start: 0.7221 (tptm) cc_final: 0.6685 (tptm) REVERT: A 64 TYR cc_start: 0.7878 (m-80) cc_final: 0.7631 (m-80) REVERT: A 79 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7315 (mm-30) REVERT: A 93 GLU cc_start: 0.7491 (tp30) cc_final: 0.6943 (tm-30) REVERT: A 119 LYS cc_start: 0.7606 (tttm) cc_final: 0.7326 (tttm) REVERT: A 138 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5994 (mm-30) REVERT: A 168 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: A 201 PHE cc_start: 0.7347 (t80) cc_final: 0.6904 (t80) REVERT: A 232 TYR cc_start: 0.6239 (t80) cc_final: 0.5832 (m-80) REVERT: A 280 LYS cc_start: 0.7293 (ttpt) cc_final: 0.6972 (ttmt) REVERT: A 298 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6953 (mp0) REVERT: A 301 LEU cc_start: 0.8089 (mt) cc_final: 0.7870 (mm) REVERT: A 317 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6543 (tp30) REVERT: A 357 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6852 (mm-30) REVERT: A 367 ASP cc_start: 0.7051 (p0) cc_final: 0.6463 (p0) REVERT: A 696 ASP cc_start: 0.6792 (m-30) cc_final: 0.6464 (m-30) REVERT: A 710 ASN cc_start: 0.7835 (m110) cc_final: 0.7346 (m-40) REVERT: A 995 GLN cc_start: 0.7005 (tp40) cc_final: 0.6658 (mp10) REVERT: A 997 THR cc_start: 0.6779 (OUTLIER) cc_final: 0.6561 (p) REVERT: A 1013 LEU cc_start: 0.8075 (tp) cc_final: 0.7786 (tm) REVERT: A 1037 ASP cc_start: 0.7182 (m-30) cc_final: 0.6758 (m-30) REVERT: A 1119 GLN cc_start: 0.7908 (mt0) cc_final: 0.7476 (mm110) REVERT: A 1124 ILE cc_start: 0.7540 (pt) cc_final: 0.7291 (pp) REVERT: A 1132 GLU cc_start: 0.7270 (mp0) cc_final: 0.6391 (mp0) REVERT: A 1133 LYS cc_start: 0.8039 (tttt) cc_final: 0.7734 (ttmt) REVERT: A 1145 ARG cc_start: 0.7179 (mtp-110) cc_final: 0.6883 (mtt-85) REVERT: A 1167 LYS cc_start: 0.8102 (tttm) cc_final: 0.7813 (tttp) REVERT: A 1186 LYS cc_start: 0.7421 (mmtm) cc_final: 0.7145 (mmtm) REVERT: A 1219 ASN cc_start: 0.7467 (t0) cc_final: 0.7075 (t0) REVERT: A 1238 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7278 (mptt) REVERT: A 1282 PHE cc_start: 0.7886 (m-80) cc_final: 0.7665 (m-80) REVERT: A 1294 SER cc_start: 0.6492 (m) cc_final: 0.6208 (t) REVERT: A 1296 GLU cc_start: 0.7753 (tt0) cc_final: 0.7279 (pt0) REVERT: A 1323 ARG cc_start: 0.6518 (ptt90) cc_final: 0.5967 (ptt90) REVERT: A 1332 ASP cc_start: 0.7262 (p0) cc_final: 0.6897 (p0) REVERT: A 1364 GLU cc_start: 0.7126 (tp30) cc_final: 0.6606 (mp0) REVERT: A 1380 TYR cc_start: 0.6799 (m-10) cc_final: 0.6462 (m-80) outliers start: 21 outliers final: 13 residues processed: 176 average time/residue: 1.3661 time to fit residues: 260.8506 Evaluate side-chains 181 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 419 ASN 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 1008 ASN 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 Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS A1301 ASN ** A1401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13503 Z= 0.278 Angle : 0.567 12.821 18840 Z= 0.304 Chirality : 0.041 0.165 2114 Planarity : 0.004 0.050 1895 Dihedral : 20.727 117.372 3239 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.72 % Allowed : 15.06 % Favored : 83.21 % 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: -0.26 (0.24), residues: 1195 helix: 0.78 (0.24), residues: 469 sheet: -0.69 (0.48), residues: 118 loop : -0.78 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 528 HIS 0.008 0.001 HIS A1033 PHE 0.021 0.001 PHE A 669 TYR 0.015 0.002 TYR A1239 ARG 0.006 0.001 ARG A 992 *********************** 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 194 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ASN cc_start: 0.6694 (m-40) cc_final: 0.6492 (m-40) REVERT: A 14 SER cc_start: 0.8039 (p) cc_final: 0.7807 (p) REVERT: A 63 LYS cc_start: 0.7227 (tptm) cc_final: 0.6686 (tptm) REVERT: A 64 TYR cc_start: 0.7878 (m-80) cc_final: 0.7636 (m-80) REVERT: A 79 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7336 (mm-30) REVERT: A 93 GLU cc_start: 0.7467 (tp30) cc_final: 0.6936 (tm-30) REVERT: A 119 LYS cc_start: 0.7611 (tttm) cc_final: 0.7332 (tttm) REVERT: A 164 SER cc_start: 0.8171 (m) cc_final: 0.7933 (p) REVERT: A 168 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: A 201 PHE cc_start: 0.7383 (t80) cc_final: 0.6853 (t80) REVERT: A 232 TYR cc_start: 0.6290 (t80) cc_final: 0.5888 (m-80) REVERT: A 280 LYS cc_start: 0.7288 (ttpt) cc_final: 0.6980 (ttmt) REVERT: A 298 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7032 (mp0) REVERT: A 301 LEU cc_start: 0.8090 (mt) cc_final: 0.7864 (mm) REVERT: A 311 LYS cc_start: 0.7898 (tppt) cc_final: 0.7386 (mmmm) REVERT: A 317 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6540 (tp30) REVERT: A 330 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 357 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6760 (mm-30) REVERT: A 367 ASP cc_start: 0.7058 (p0) cc_final: 0.6466 (p0) REVERT: A 710 ASN cc_start: 0.7794 (m110) cc_final: 0.7297 (m-40) REVERT: A 980 ASP cc_start: 0.6525 (OUTLIER) cc_final: 0.6310 (t0) REVERT: A 995 GLN cc_start: 0.6967 (tp40) cc_final: 0.6684 (mp10) REVERT: A 997 THR cc_start: 0.6781 (OUTLIER) cc_final: 0.6508 (p) REVERT: A 1013 LEU cc_start: 0.8085 (tp) cc_final: 0.7772 (tm) REVERT: A 1037 ASP cc_start: 0.7188 (m-30) cc_final: 0.6764 (m-30) REVERT: A 1119 GLN cc_start: 0.7933 (mt0) cc_final: 0.7489 (mm110) REVERT: A 1124 ILE cc_start: 0.7479 (pt) cc_final: 0.7240 (pp) REVERT: A 1132 GLU cc_start: 0.7302 (mp0) cc_final: 0.6470 (mp0) REVERT: A 1133 LYS cc_start: 0.8056 (tttt) cc_final: 0.7741 (ttmt) REVERT: A 1145 ARG cc_start: 0.7181 (mtp-110) cc_final: 0.6925 (mtt-85) REVERT: A 1186 LYS cc_start: 0.7423 (mmtm) cc_final: 0.7142 (mmtm) REVERT: A 1219 ASN cc_start: 0.7483 (t0) cc_final: 0.7092 (t0) REVERT: A 1238 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7241 (mptt) REVERT: A 1282 PHE cc_start: 0.7896 (m-80) cc_final: 0.7654 (m-80) REVERT: A 1294 SER cc_start: 0.6490 (m) cc_final: 0.6150 (t) REVERT: A 1296 GLU cc_start: 0.7714 (tt0) cc_final: 0.7004 (pt0) REVERT: A 1323 ARG cc_start: 0.6456 (ptt90) cc_final: 0.5930 (ptt90) REVERT: A 1332 ASP cc_start: 0.7244 (p0) cc_final: 0.6890 (p0) REVERT: A 1364 GLU cc_start: 0.7130 (tp30) cc_final: 0.6601 (mp0) REVERT: A 1380 TYR cc_start: 0.6825 (m-10) cc_final: 0.6445 (m-80) outliers start: 19 outliers final: 12 residues processed: 182 average time/residue: 1.3121 time to fit residues: 259.2186 Evaluate side-chains 188 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 173 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 168 GLU 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 1008 ASN 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 1301 ASN Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.0570 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 0.2980 chunk 110 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 ** A1401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.4888 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= 0.213 Angle : 0.545 15.002 18840 Z= 0.290 Chirality : 0.039 0.165 2114 Planarity : 0.004 0.047 1895 Dihedral : 20.686 117.187 3239 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.54 % Allowed : 16.06 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.24), residues: 469 sheet: -0.59 (0.49), residues: 121 loop : -0.76 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 528 HIS 0.007 0.001 HIS A1033 PHE 0.015 0.001 PHE A 990 TYR 0.014 0.001 TYR A1239 ARG 0.004 0.000 ARG A 350 ********************** 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 189 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 SER cc_start: 0.8008 (p) cc_final: 0.7785 (p) REVERT: A 63 LYS cc_start: 0.7216 (tptm) cc_final: 0.6690 (tptm) REVERT: A 64 TYR cc_start: 0.7864 (m-80) cc_final: 0.7626 (m-80) REVERT: A 79 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7322 (mm-30) REVERT: A 93 GLU cc_start: 0.7490 (tp30) cc_final: 0.6946 (tm-30) REVERT: A 119 LYS cc_start: 0.7589 (tttm) cc_final: 0.7314 (tttm) REVERT: A 168 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: A 201 PHE cc_start: 0.7336 (t80) cc_final: 0.6865 (t80) REVERT: A 232 TYR cc_start: 0.6255 (t80) cc_final: 0.5840 (m-80) REVERT: A 280 LYS cc_start: 0.7299 (ttpt) cc_final: 0.7008 (ttmt) REVERT: A 298 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6990 (mp0) REVERT: A 301 LEU cc_start: 0.8093 (mt) cc_final: 0.7878 (mm) REVERT: A 317 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6552 (tp30) REVERT: A 330 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 357 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 367 ASP cc_start: 0.7038 (p0) cc_final: 0.6449 (p0) REVERT: A 710 ASN cc_start: 0.7829 (m110) cc_final: 0.7280 (m-40) REVERT: A 980 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.6292 (t0) REVERT: A 995 GLN cc_start: 0.6942 (tp40) cc_final: 0.6589 (mp10) REVERT: A 997 THR cc_start: 0.6769 (OUTLIER) cc_final: 0.6501 (p) REVERT: A 1013 LEU cc_start: 0.8023 (tp) cc_final: 0.7725 (tm) REVERT: A 1037 ASP cc_start: 0.7157 (m-30) cc_final: 0.6719 (m-30) REVERT: A 1119 GLN cc_start: 0.7908 (mt0) cc_final: 0.7470 (mm110) REVERT: A 1124 ILE cc_start: 0.7508 (pt) cc_final: 0.7257 (pp) REVERT: A 1132 GLU cc_start: 0.7250 (mp0) cc_final: 0.6455 (mp0) REVERT: A 1145 ARG cc_start: 0.7180 (mtp-110) cc_final: 0.6878 (mtt-85) REVERT: A 1186 LYS cc_start: 0.7404 (mmtm) cc_final: 0.7136 (mmtm) REVERT: A 1219 ASN cc_start: 0.7478 (t0) cc_final: 0.7072 (t0) REVERT: A 1282 PHE cc_start: 0.7874 (m-80) cc_final: 0.7616 (m-80) REVERT: A 1294 SER cc_start: 0.6580 (m) cc_final: 0.6218 (t) REVERT: A 1296 GLU cc_start: 0.7758 (tt0) cc_final: 0.7047 (pt0) REVERT: A 1323 ARG cc_start: 0.6500 (ptt90) cc_final: 0.5960 (ptt90) REVERT: A 1364 GLU cc_start: 0.7084 (tp30) cc_final: 0.6627 (mp0) REVERT: A 1380 TYR cc_start: 0.6743 (m-10) cc_final: 0.6372 (m-80) outliers start: 17 outliers final: 9 residues processed: 178 average time/residue: 1.3623 time to fit residues: 262.4995 Evaluate side-chains 179 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 419 ASN 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 1008 ASN Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1366 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 A1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.226170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.181574 restraints weight = 41812.183| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 5.60 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4167 r_free = 0.4167 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 = 0.4167 r_free = 0.4167 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.5022 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= 0.255 Angle : 0.579 14.044 18840 Z= 0.305 Chirality : 0.040 0.165 2114 Planarity : 0.004 0.049 1895 Dihedral : 20.708 117.293 3239 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.72 % Allowed : 16.15 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.24), residues: 1195 helix: 0.89 (0.24), residues: 469 sheet: -0.81 (0.45), residues: 128 loop : -0.77 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 528 HIS 0.007 0.001 HIS A1033 PHE 0.015 0.001 PHE A 990 TYR 0.015 0.001 TYR A1239 ARG 0.005 0.000 ARG A 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4891.89 seconds wall clock time: 86 minutes 25.02 seconds (5185.02 seconds total)