Starting phenix.real_space_refine on Sat Jul 20 08:56:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6s_41079/07_2024/8t6s_41079.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6s_41079/07_2024/8t6s_41079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6s_41079/07_2024/8t6s_41079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6s_41079/07_2024/8t6s_41079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6s_41079/07_2024/8t6s_41079.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6s_41079/07_2024/8t6s_41079.cif" } resolution = 3.28 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= -0.000 sd= 0.009 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 119 5.49 5 S 14 5.16 5 C 6185 2.51 5 N 1839 2.21 5 O 2243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10400 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7878 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 28, 'TRANS': 933} Chain breaks: 9 Chain: "B" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1931 Classifications: {'RNA': 90} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 79} Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 7.69, per 1000 atoms: 0.74 Number of scatterers: 10400 At special positions: 0 Unit cell: (87.486, 119.981, 119.981, 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 14 16.00 P 119 15.00 O 2243 8.00 N 1839 7.00 C 6185 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: 4.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 56.4% alpha, 6.5% beta 41 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.694A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.679A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.616A pdb=" N ASN A 178 " --> pdb=" O ASN A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 190 removed outlier: 3.928A pdb=" N LEU A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.521A pdb=" N GLN A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 4.267A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 344 through 353 removed outlier: 4.159A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.080A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.105A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.843A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.672A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.620A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 Processing helix chain 'A' and resid 593 through 602 removed outlier: 4.317A pdb=" N LEU A 598 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS A 599 " --> pdb=" O HIS A 595 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.796A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 5.144A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 643 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 4.173A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.520A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.201A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1000 removed outlier: 4.409A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1087 removed outlier: 4.526A pdb=" N ARG A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.572A pdb=" N GLY A1132 " --> pdb=" O PRO A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.228A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 removed outlier: 3.534A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1260 Processing helix chain 'A' and resid 1261 through 1263 No H-bonds generated for 'chain 'A' and resid 1261 through 1263' Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 4.759A pdb=" N ILE A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1297 removed outlier: 3.697A pdb=" N ASP A1288 " --> pdb=" O ASP A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1339 through 1343 removed outlier: 3.554A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.662A pdb=" N GLY A 17 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 48 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A1095 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA A 50 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.583A pdb=" N LYS A 30 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 509 Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.502A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1219 through 1222 removed outlier: 6.278A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 5.37 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: 2222 1.33 - 1.45: 2904 1.45 - 1.57: 5454 1.57 - 1.69: 235 1.69 - 1.81: 27 Bond restraints: 10842 Sorted by residual: bond pdb=" CD1 TYR A 981 " pdb=" CE1 TYR A 981 " ideal model delta sigma weight residual 1.382 1.283 0.099 3.00e-02 1.11e+03 1.08e+01 bond pdb=" CB TYR A 981 " pdb=" CG TYR A 981 " ideal model delta sigma weight residual 1.512 1.454 0.058 2.20e-02 2.07e+03 6.89e+00 bond pdb=" CG1 ILE A 619 " pdb=" CD1 ILE A 619 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.04e+00 bond pdb=" CB VAL A1092 " pdb=" CG1 VAL A1092 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.67e+00 bond pdb=" CB ARG A 976 " pdb=" CG ARG A 976 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.00e+00 ... (remaining 10837 not shown) Histogram of bond angle deviations from ideal: 95.82 - 103.49: 336 103.49 - 111.16: 4568 111.16 - 118.83: 4538 118.83 - 126.50: 5271 126.50 - 134.17: 438 Bond angle restraints: 15151 Sorted by residual: angle pdb=" CG1 VAL A1092 " pdb=" CB VAL A1092 " pdb=" CG2 VAL A1092 " ideal model delta sigma weight residual 110.80 96.85 13.95 2.20e+00 2.07e-01 4.02e+01 angle pdb=" CA ILE A 619 " pdb=" CB ILE A 619 " pdb=" CG1 ILE A 619 " ideal model delta sigma weight residual 110.40 119.30 -8.90 1.70e+00 3.46e-01 2.74e+01 angle pdb=" CB MET A 648 " pdb=" CG MET A 648 " pdb=" SD MET A 648 " ideal model delta sigma weight residual 112.70 127.59 -14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O3' DG C 22 " pdb=" P DT C 23 " pdb=" OP1 DT C 23 " ideal model delta sigma weight residual 108.00 121.87 -13.87 3.00e+00 1.11e-01 2.14e+01 angle pdb=" CA LEU A1312 " pdb=" CB LEU A1312 " pdb=" CG LEU A1312 " ideal model delta sigma weight residual 116.30 132.41 -16.11 3.50e+00 8.16e-02 2.12e+01 ... (remaining 15146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.72: 6039 29.72 - 59.45: 464 59.45 - 89.17: 96 89.17 - 118.89: 1 118.89 - 148.62: 1 Dihedral angle restraints: 6601 sinusoidal: 3780 harmonic: 2821 Sorted by residual: dihedral pdb=" CA SER A1106 " pdb=" C SER A1106 " pdb=" N LYS A1107 " pdb=" CA LYS A1107 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA SER A 512 " pdb=" C SER A 512 " pdb=" N LEU A 513 " pdb=" CA LEU A 513 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA THR A 22 " pdb=" C THR A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta harmonic sigma weight residual -180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 6598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1666 0.109 - 0.217: 78 0.217 - 0.326: 10 0.326 - 0.434: 5 0.434 - 0.543: 2 Chirality restraints: 1761 Sorted by residual: chirality pdb=" CG LEU A1312 " pdb=" CB LEU A1312 " pdb=" CD1 LEU A1312 " pdb=" CD2 LEU A1312 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" P DT C 23 " pdb=" OP1 DT C 23 " pdb=" OP2 DT C 23 " pdb=" O5' DT C 23 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CG LEU A 301 " pdb=" CB LEU A 301 " pdb=" CD1 LEU A 301 " pdb=" CD2 LEU A 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 1758 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC C 29 " 0.020 2.00e-02 2.50e+03 3.80e-02 3.25e+01 pdb=" N1 DC C 29 " -0.055 2.00e-02 2.50e+03 pdb=" C2 DC C 29 " 0.088 2.00e-02 2.50e+03 pdb=" O2 DC C 29 " -0.039 2.00e-02 2.50e+03 pdb=" N3 DC C 29 " -0.015 2.00e-02 2.50e+03 pdb=" C4 DC C 29 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC C 29 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC C 29 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC C 29 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 32 " 0.016 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE A 32 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 32 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 32 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE A 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 32 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 32 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 66 " 0.023 2.00e-02 2.50e+03 2.41e-02 1.30e+01 pdb=" N1 U B 66 " -0.057 2.00e-02 2.50e+03 pdb=" C2 U B 66 " 0.035 2.00e-02 2.50e+03 pdb=" O2 U B 66 " -0.011 2.00e-02 2.50e+03 pdb=" N3 U B 66 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U B 66 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U B 66 " 0.002 2.00e-02 2.50e+03 pdb=" C5 U B 66 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U B 66 " 0.008 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1363 2.75 - 3.29: 10315 3.29 - 3.83: 19208 3.83 - 4.36: 22535 4.36 - 4.90: 33906 Nonbonded interactions: 87327 Sorted by model distance: nonbonded pdb=" O ARG A 69 " pdb=" OG1 THR A 73 " model vdw 2.217 2.440 nonbonded pdb=" O ARG A1337 " pdb=" NH1 ARG A1337 " model vdw 2.221 2.520 nonbonded pdb=" OE2 GLU A 505 " pdb=" OG SER A 663 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.223 2.440 nonbonded pdb=" OG SER A 512 " pdb=" OE1 GLU A 617 " model vdw 2.254 2.440 ... (remaining 87322 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=0.00 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 36.920 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.006 0.099 10842 Z= 0.360 Angle : 1.062 16.113 15151 Z= 0.541 Chirality : 0.060 0.543 1761 Planarity : 0.008 0.106 1483 Dihedral : 19.307 148.617 4769 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.12 % Allowed : 20.02 % Favored : 79.86 % 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: -1.45 (0.26), residues: 942 helix: -0.96 (0.22), residues: 447 sheet: -0.79 (0.59), residues: 80 loop : -0.81 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.005 TRP A 18 HIS 0.017 0.002 HIS A1241 PHE 0.060 0.003 PHE A 32 TYR 0.038 0.003 TYR A 136 ARG 0.024 0.002 ARG A1111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9064 (mt) cc_final: 0.8710 (tt) REVERT: A 498 PHE cc_start: 0.8173 (m-80) cc_final: 0.7923 (m-10) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2736 time to fit residues: 31.6169 Evaluate side-chains 71 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10842 Z= 0.338 Angle : 0.689 7.848 15151 Z= 0.363 Chirality : 0.041 0.337 1761 Planarity : 0.005 0.057 1483 Dihedral : 19.920 153.665 2723 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.17 % Allowed : 15.28 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.26), residues: 942 helix: -0.04 (0.24), residues: 451 sheet: -0.36 (0.70), residues: 60 loop : -0.91 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 18 HIS 0.011 0.001 HIS A 167 PHE 0.029 0.002 PHE A 32 TYR 0.019 0.002 TYR A 515 ARG 0.007 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 80 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9301 (mt) cc_final: 0.9072 (tt) REVERT: A 165 ARG cc_start: 0.8487 (ptt90) cc_final: 0.8272 (ptt90) REVERT: A 301 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8657 (mm) REVERT: A 495 MET cc_start: 0.7904 (ppp) cc_final: 0.7678 (ppp) REVERT: A 649 LYS cc_start: 0.9534 (mttm) cc_final: 0.9330 (ptmm) REVERT: A 1297 HIS cc_start: 0.8515 (m90) cc_final: 0.8282 (m90) REVERT: A 1352 ILE cc_start: 0.9009 (mp) cc_final: 0.8664 (tp) outliers start: 36 outliers final: 25 residues processed: 105 average time/residue: 0.2296 time to fit residues: 34.2872 Evaluate side-chains 95 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 26 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10842 Z= 0.182 Angle : 0.558 7.086 15151 Z= 0.297 Chirality : 0.037 0.246 1761 Planarity : 0.004 0.057 1483 Dihedral : 19.713 151.430 2723 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.55 % Allowed : 17.71 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.27), residues: 942 helix: 0.47 (0.24), residues: 449 sheet: -0.29 (0.70), residues: 60 loop : -0.78 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1136 HIS 0.008 0.001 HIS A1241 PHE 0.027 0.002 PHE A1313 TYR 0.023 0.002 TYR A 515 ARG 0.004 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9399 (mt) cc_final: 0.9182 (tt) REVERT: A 301 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8515 (mm) REVERT: A 648 MET cc_start: 0.8128 (ppp) cc_final: 0.7652 (ppp) REVERT: A 1297 HIS cc_start: 0.8461 (m90) cc_final: 0.8219 (m90) REVERT: A 1356 TYR cc_start: 0.8079 (m-80) cc_final: 0.7315 (m-80) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.2865 time to fit residues: 38.5633 Evaluate side-chains 86 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10842 Z= 0.309 Angle : 0.638 9.130 15151 Z= 0.335 Chirality : 0.039 0.230 1761 Planarity : 0.004 0.059 1483 Dihedral : 19.886 153.447 2723 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.17 % Allowed : 17.36 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.27), residues: 942 helix: 0.45 (0.24), residues: 449 sheet: -0.62 (0.71), residues: 60 loop : -0.80 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1136 HIS 0.010 0.001 HIS A 167 PHE 0.024 0.002 PHE A1105 TYR 0.016 0.002 TYR A 981 ARG 0.008 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 68 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 498 PHE cc_start: 0.8315 (m-10) cc_final: 0.8085 (m-80) REVERT: A 1297 HIS cc_start: 0.8553 (m90) cc_final: 0.8325 (m90) REVERT: A 1352 ILE cc_start: 0.9018 (mp) cc_final: 0.8695 (tp) outliers start: 36 outliers final: 27 residues processed: 94 average time/residue: 0.2510 time to fit residues: 32.9374 Evaluate side-chains 92 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10842 Z= 0.177 Angle : 0.551 7.838 15151 Z= 0.290 Chirality : 0.036 0.210 1761 Planarity : 0.004 0.057 1483 Dihedral : 19.724 151.385 2723 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.36 % Allowed : 19.10 % Favored : 77.55 % 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: 0.00 (0.27), residues: 942 helix: 0.73 (0.25), residues: 448 sheet: -0.53 (0.72), residues: 60 loop : -0.62 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1136 HIS 0.006 0.001 HIS A1311 PHE 0.025 0.001 PHE A1105 TYR 0.015 0.001 TYR A 155 ARG 0.005 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 74 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7534 (tp) cc_final: 0.7062 (tp) REVERT: A 1297 HIS cc_start: 0.8596 (m90) cc_final: 0.8349 (m90) REVERT: A 1337 ARG cc_start: 0.7292 (tpt90) cc_final: 0.7089 (tpt90) outliers start: 29 outliers final: 24 residues processed: 97 average time/residue: 0.2426 time to fit residues: 33.0563 Evaluate side-chains 94 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.0070 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10842 Z= 0.227 Angle : 0.575 7.135 15151 Z= 0.302 Chirality : 0.037 0.196 1761 Planarity : 0.004 0.057 1483 Dihedral : 19.742 152.138 2723 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.17 % Allowed : 18.17 % Favored : 77.66 % 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: -0.02 (0.27), residues: 942 helix: 0.72 (0.25), residues: 452 sheet: -0.62 (0.72), residues: 60 loop : -0.62 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.007 0.001 HIS A 167 PHE 0.025 0.002 PHE A1313 TYR 0.013 0.001 TYR A 515 ARG 0.006 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 72 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7598 (ptpp) REVERT: A 1297 HIS cc_start: 0.8629 (m90) cc_final: 0.8278 (m90) outliers start: 36 outliers final: 29 residues processed: 99 average time/residue: 0.2412 time to fit residues: 33.2958 Evaluate side-chains 100 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 70 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 10842 Z= 0.561 Angle : 0.854 10.482 15151 Z= 0.442 Chirality : 0.047 0.265 1761 Planarity : 0.006 0.070 1483 Dihedral : 20.357 156.497 2723 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 28.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.51 % Allowed : 19.21 % Favored : 76.27 % 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: -0.96 (0.26), residues: 942 helix: -0.17 (0.23), residues: 453 sheet: -0.95 (0.73), residues: 60 loop : -0.98 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 464 HIS 0.017 0.002 HIS A 167 PHE 0.028 0.003 PHE A1105 TYR 0.042 0.003 TYR A 25 ARG 0.008 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 62 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7621 (t-170) REVERT: A 500 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7574 (ptpp) REVERT: A 648 MET cc_start: 0.8381 (ppp) cc_final: 0.8142 (ppp) REVERT: A 751 MET cc_start: 0.8381 (mmm) cc_final: 0.8123 (mmm) REVERT: A 1169 MET cc_start: 0.7460 (mmt) cc_final: 0.6713 (mmt) REVERT: A 1297 HIS cc_start: 0.8627 (m90) cc_final: 0.8297 (m90) REVERT: A 1352 ILE cc_start: 0.9126 (mp) cc_final: 0.8858 (tp) outliers start: 39 outliers final: 31 residues processed: 91 average time/residue: 0.2401 time to fit residues: 31.7829 Evaluate side-chains 91 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 58 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 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 46 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10842 Z= 0.174 Angle : 0.581 9.187 15151 Z= 0.302 Chirality : 0.037 0.218 1761 Planarity : 0.004 0.056 1483 Dihedral : 19.880 151.014 2723 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.70 % Allowed : 21.06 % Favored : 75.23 % 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: -0.24 (0.27), residues: 942 helix: 0.50 (0.25), residues: 450 sheet: -1.02 (0.71), residues: 60 loop : -0.64 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1136 HIS 0.012 0.001 HIS A1241 PHE 0.016 0.001 PHE A 972 TYR 0.019 0.002 TYR A 25 ARG 0.010 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7761 (tp) cc_final: 0.7293 (tp) REVERT: A 648 MET cc_start: 0.8334 (ppp) cc_final: 0.8094 (ppp) REVERT: A 1297 HIS cc_start: 0.8625 (m90) cc_final: 0.8287 (m90) REVERT: A 1312 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9186 (mm) REVERT: A 1356 TYR cc_start: 0.8132 (m-10) cc_final: 0.7630 (m-80) outliers start: 32 outliers final: 26 residues processed: 98 average time/residue: 0.2227 time to fit residues: 31.3562 Evaluate side-chains 97 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10842 Z= 0.358 Angle : 0.687 7.906 15151 Z= 0.358 Chirality : 0.040 0.214 1761 Planarity : 0.005 0.058 1483 Dihedral : 20.045 153.537 2723 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.12 % Allowed : 20.95 % Favored : 75.93 % 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: -0.60 (0.27), residues: 942 helix: 0.22 (0.24), residues: 459 sheet: -1.13 (0.70), residues: 60 loop : -0.88 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.012 0.001 HIS A 167 PHE 0.018 0.002 PHE A1105 TYR 0.021 0.002 TYR A 25 ARG 0.007 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1297 HIS cc_start: 0.8596 (m90) cc_final: 0.8272 (m90) REVERT: A 1312 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9227 (mm) REVERT: A 1325 LYS cc_start: 0.8910 (tmmt) cc_final: 0.8564 (tmmt) REVERT: A 1352 ILE cc_start: 0.8970 (mp) cc_final: 0.8754 (tp) outliers start: 27 outliers final: 25 residues processed: 86 average time/residue: 0.2154 time to fit residues: 27.2871 Evaluate side-chains 90 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 64 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10842 Z= 0.463 Angle : 0.779 9.564 15151 Z= 0.405 Chirality : 0.044 0.247 1761 Planarity : 0.005 0.059 1483 Dihedral : 20.324 155.229 2723 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 26.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.59 % Allowed : 21.18 % Favored : 75.23 % 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: -1.11 (0.27), residues: 942 helix: -0.21 (0.23), residues: 455 sheet: -1.38 (0.69), residues: 60 loop : -1.13 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A1136 HIS 0.015 0.002 HIS A 167 PHE 0.022 0.002 PHE A1105 TYR 0.025 0.002 TYR A 25 ARG 0.006 0.001 ARG A 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 62 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7694 (t-170) REVERT: A 321 MET cc_start: 0.8806 (mmt) cc_final: 0.8251 (mmt) REVERT: A 751 MET cc_start: 0.8398 (mmm) cc_final: 0.8193 (mmm) REVERT: A 1297 HIS cc_start: 0.8559 (m90) cc_final: 0.8272 (m90) REVERT: A 1325 LYS cc_start: 0.8893 (tmmt) cc_final: 0.8569 (tmmt) REVERT: A 1352 ILE cc_start: 0.9093 (mp) cc_final: 0.8865 (tp) outliers start: 31 outliers final: 26 residues processed: 82 average time/residue: 0.2048 time to fit residues: 25.0636 Evaluate side-chains 86 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 59 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 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 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.102961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.074110 restraints weight = 37110.644| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 4.15 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10842 Z= 0.169 Angle : 0.607 10.074 15151 Z= 0.314 Chirality : 0.038 0.211 1761 Planarity : 0.004 0.055 1483 Dihedral : 19.916 150.208 2723 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.31 % Allowed : 22.80 % Favored : 74.88 % 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: -0.49 (0.27), residues: 942 helix: 0.42 (0.24), residues: 458 sheet: -1.36 (0.72), residues: 52 loop : -0.94 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1136 HIS 0.014 0.001 HIS A1241 PHE 0.014 0.001 PHE A 972 TYR 0.020 0.002 TYR A1242 ARG 0.011 0.001 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.35 seconds wall clock time: 37 minutes 49.52 seconds (2269.52 seconds total)