Starting phenix.real_space_refine on Fri Jan 19 00:50:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/01_2024/7s3h_24823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/01_2024/7s3h_24823.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/01_2024/7s3h_24823_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/01_2024/7s3h_24823_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/01_2024/7s3h_24823_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/01_2024/7s3h_24823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/01_2024/7s3h_24823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/01_2024/7s3h_24823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/01_2024/7s3h_24823_updated.pdb" } resolution = 2.5 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= 0.149 sd= 0.899 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 75 5.49 5 S 18 5.16 5 C 6067 2.51 5 N 1755 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9966 Number of models: 1 Model: "" Number of chains: 4 Chain: "N" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 479 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "P" Number of atoms: 8378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8378 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 26, 'TRANS': 1003} Chain breaks: 3 Chain: "R" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 645 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna2p': 4, 'rna3p': 25} Chain: "T" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 464 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.25, per 1000 atoms: 0.63 Number of scatterers: 9966 At special positions: 0 Unit cell: (91.35, 114.45, 116.55, 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 18 16.00 P 75 15.00 O 2051 8.00 N 1755 7.00 C 6067 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 8 sheets defined 47.9% alpha, 9.3% beta 32 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 5.69 Creating SS restraints... Processing helix chain 'P' and resid 59 through 63 Processing helix chain 'P' and resid 68 through 90 removed outlier: 4.760A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 131 Processing helix chain 'P' and resid 135 through 144 Processing helix chain 'P' and resid 151 through 163 Processing helix chain 'P' and resid 176 through 178 No H-bonds generated for 'chain 'P' and resid 176 through 178' Processing helix chain 'P' and resid 181 through 196 Processing helix chain 'P' and resid 208 through 212 Processing helix chain 'P' and resid 218 through 227 Processing helix chain 'P' and resid 237 through 246 Processing helix chain 'P' and resid 253 through 256 No H-bonds generated for 'chain 'P' and resid 253 through 256' Processing helix chain 'P' and resid 271 through 282 Processing helix chain 'P' and resid 284 through 307 removed outlier: 4.500A pdb=" N ASP P 288 " --> pdb=" O GLN P 285 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE P 305 " --> pdb=" O LEU P 302 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU P 306 " --> pdb=" O SER P 303 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG P 307 " --> pdb=" O ASP P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 316 through 342 Processing helix chain 'P' and resid 347 through 351 Processing helix chain 'P' and resid 359 through 363 Processing helix chain 'P' and resid 369 through 382 Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 389 through 394 Processing helix chain 'P' and resid 405 through 409 removed outlier: 3.765A pdb=" N GLY P 408 " --> pdb=" O PHE P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 412 through 425 Processing helix chain 'P' and resid 431 through 435 Processing helix chain 'P' and resid 437 through 445 Processing helix chain 'P' and resid 720 through 725 Processing helix chain 'P' and resid 731 through 750 Processing helix chain 'P' and resid 773 through 791 removed outlier: 3.934A pdb=" N SER P 777 " --> pdb=" O GLY P 773 " (cutoff:3.500A) Processing helix chain 'P' and resid 795 through 798 No H-bonds generated for 'chain 'P' and resid 795 through 798' Processing helix chain 'P' and resid 805 through 807 No H-bonds generated for 'chain 'P' and resid 805 through 807' Processing helix chain 'P' and resid 809 through 816 Processing helix chain 'P' and resid 852 through 854 No H-bonds generated for 'chain 'P' and resid 852 through 854' Processing helix chain 'P' and resid 861 through 864 removed outlier: 3.660A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 861 through 864' Processing helix chain 'P' and resid 873 through 888 removed outlier: 3.876A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR P 882 " --> pdb=" O LYS P 878 " (cutoff:3.500A) Processing helix chain 'P' and resid 894 through 900 Processing helix chain 'P' and resid 903 through 905 No H-bonds generated for 'chain 'P' and resid 903 through 905' Processing helix chain 'P' and resid 910 through 921 Processing helix chain 'P' and resid 926 through 939 Processing helix chain 'P' and resid 960 through 969 Processing helix chain 'P' and resid 981 through 1000 Processing helix chain 'P' and resid 1002 through 1008 removed outlier: 4.684A pdb=" N SER P1006 " --> pdb=" O LYS P1003 " (cutoff:3.500A) Processing helix chain 'P' and resid 1042 through 1044 No H-bonds generated for 'chain 'P' and resid 1042 through 1044' Processing helix chain 'P' and resid 1078 through 1088 Processing helix chain 'P' and resid 1171 through 1176 Processing helix chain 'P' and resid 1178 through 1185 Processing helix chain 'P' and resid 1192 through 1194 No H-bonds generated for 'chain 'P' and resid 1192 through 1194' Processing helix chain 'P' and resid 1207 through 1209 No H-bonds generated for 'chain 'P' and resid 1207 through 1209' Processing helix chain 'P' and resid 1230 through 1240 Processing helix chain 'P' and resid 1249 through 1261 Processing helix chain 'P' and resid 1263 through 1280 removed outlier: 3.606A pdb=" N PHE P1276 " --> pdb=" O ILE P1273 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL P1280 " --> pdb=" O SER P1277 " (cutoff:3.500A) Processing helix chain 'P' and resid 1284 through 1296 Processing helix chain 'P' and resid 1302 through 1315 removed outlier: 4.610A pdb=" N THR P1314 " --> pdb=" O ILE P1310 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU P1315 " --> pdb=" O HIS P1311 " (cutoff:3.500A) Processing helix chain 'P' and resid 1341 through 1344 Processing sheet with id= A, first strand: chain 'P' and resid 954 through 958 removed outlier: 4.760A pdb=" N MET P 763 " --> pdb=" O LEU P 958 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASN P1093 " --> pdb=" O ALA P 50 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU P 52 " --> pdb=" O ASN P1093 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL P1095 " --> pdb=" O LEU P 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'P' and resid 29 through 33 Processing sheet with id= C, first strand: chain 'P' and resid 34 through 36 removed outlier: 7.031A pdb=" N GLU P1357 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU P1203 " --> pdb=" O ILE P1348 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 837 through 840 Processing sheet with id= E, first strand: chain 'P' and resid 1049 through 1051 Processing sheet with id= F, first strand: chain 'P' and resid 1196 through 1198 removed outlier: 7.232A pdb=" N ILE P1166 " --> pdb=" O ALA P1140 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER P1142 " --> pdb=" O LEU P1164 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU P1164 " --> pdb=" O SER P1142 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU P1144 " --> pdb=" O GLU P1162 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU P1162 " --> pdb=" O LEU P1144 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL P1146 " --> pdb=" O VAL P1160 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL P1160 " --> pdb=" O VAL P1146 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS P1148 " --> pdb=" O LYS P1158 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS P1158 " --> pdb=" O LYS P1148 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU P1150 " --> pdb=" O LYS P1156 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS P1156 " --> pdb=" O GLU P1150 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'P' and resid 1324 through 1326 Processing sheet with id= H, first strand: chain 'P' and resid 1063 through 1065 337 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2536 1.34 - 1.46: 2210 1.46 - 1.58: 5360 1.58 - 1.70: 154 1.70 - 1.82: 33 Bond restraints: 10293 Sorted by residual: bond pdb=" C2' 2YR T 6 " pdb=" C3' 2YR T 6 " ideal model delta sigma weight residual 1.224 1.518 -0.294 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C4' 2YR T 6 " pdb=" O4' 2YR T 6 " ideal model delta sigma weight residual 1.271 1.465 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C1' 2YR T 6 " pdb=" N1 2YR T 6 " ideal model delta sigma weight residual 1.348 1.527 -0.179 2.00e-02 2.50e+03 7.98e+01 bond pdb=" C5 2YR T 6 " pdb=" C6 2YR T 6 " ideal model delta sigma weight residual 1.499 1.336 0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C4 2YR T 6 " pdb=" N4 2YR T 6 " ideal model delta sigma weight residual 1.477 1.343 0.134 2.00e-02 2.50e+03 4.48e+01 ... (remaining 10288 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.47: 496 105.47 - 112.60: 5123 112.60 - 119.73: 3825 119.73 - 126.86: 4476 126.86 - 133.99: 269 Bond angle restraints: 14189 Sorted by residual: angle pdb=" C2' DT T 11 " pdb=" C1' DT T 11 " pdb=" N1 DT T 11 " ideal model delta sigma weight residual 113.50 119.22 -5.72 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C2' DT T 5 " pdb=" C1' DT T 5 " pdb=" N1 DT T 5 " ideal model delta sigma weight residual 113.50 119.02 -5.52 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C2' DC T 9 " pdb=" C1' DC T 9 " pdb=" N1 DC T 9 " ideal model delta sigma weight residual 113.50 119.01 -5.51 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C2' DC T 15 " pdb=" C1' DC T 15 " pdb=" N1 DC T 15 " ideal model delta sigma weight residual 113.50 118.98 -5.48 1.50e+00 4.44e-01 1.34e+01 angle pdb=" C2' DT T 12 " pdb=" C1' DT T 12 " pdb=" N1 DT T 12 " ideal model delta sigma weight residual 113.50 118.94 -5.44 1.50e+00 4.44e-01 1.32e+01 ... (remaining 14184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.17: 5779 32.17 - 64.34: 405 64.34 - 96.52: 24 96.52 - 128.69: 0 128.69 - 160.86: 1 Dihedral angle restraints: 6209 sinusoidal: 3179 harmonic: 3030 Sorted by residual: dihedral pdb=" C3' 2YR T 6 " pdb=" C4' 2YR T 6 " pdb=" C5' 2YR T 6 " pdb=" O5' 2YR T 6 " ideal model delta sinusoidal sigma weight residual 191.74 30.88 160.86 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CA GLU P 198 " pdb=" C GLU P 198 " pdb=" N ASN P 199 " pdb=" CA ASN P 199 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA P1215 " pdb=" C ALA P1215 " pdb=" N SER P1216 " pdb=" CA SER P1216 " ideal model delta harmonic sigma weight residual 180.00 -161.73 -18.27 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 6206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1184 0.052 - 0.104: 343 0.104 - 0.156: 68 0.156 - 0.209: 7 0.209 - 0.261: 3 Chirality restraints: 1605 Sorted by residual: chirality pdb=" C3' 2YR T 6 " pdb=" C2' 2YR T 6 " pdb=" C4' 2YR T 6 " pdb=" O3' 2YR T 6 " both_signs ideal model delta sigma weight residual False -2.39 -2.65 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL P 143 " pdb=" CA VAL P 143 " pdb=" CG1 VAL P 143 " pdb=" CG2 VAL P 143 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE P 956 " pdb=" CA ILE P 956 " pdb=" CG1 ILE P 956 " pdb=" CG2 ILE P 956 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1602 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2YR T 6 " -0.040 2.00e-02 2.50e+03 7.32e-02 1.34e+02 pdb=" C2 2YR T 6 " -0.006 2.00e-02 2.50e+03 pdb=" C4 2YR T 6 " 0.061 2.00e-02 2.50e+03 pdb=" C5 2YR T 6 " 0.068 2.00e-02 2.50e+03 pdb=" C6 2YR T 6 " 0.028 2.00e-02 2.50e+03 pdb=" C9 2YR T 6 " -0.171 2.00e-02 2.50e+03 pdb=" N1 2YR T 6 " -0.024 2.00e-02 2.50e+03 pdb=" N3 2YR T 6 " 0.028 2.00e-02 2.50e+03 pdb=" N4 2YR T 6 " 0.101 2.00e-02 2.50e+03 pdb=" O2 2YR T 6 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 17 " 0.055 2.00e-02 2.50e+03 3.29e-02 2.99e+01 pdb=" N9 DA N 17 " -0.084 2.00e-02 2.50e+03 pdb=" C8 DA N 17 " 0.032 2.00e-02 2.50e+03 pdb=" N7 DA N 17 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA N 17 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DA N 17 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA N 17 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DA N 17 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DA N 17 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA N 17 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA N 17 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 284 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ASP P 284 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP P 284 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN P 285 " -0.023 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1364 2.77 - 3.30: 9450 3.30 - 3.83: 16957 3.83 - 4.37: 20680 4.37 - 4.90: 32750 Nonbonded interactions: 81201 Sorted by model distance: nonbonded pdb=" NH2 ARG P 139 " pdb=" OE1 GLU P 418 " model vdw 2.234 2.520 nonbonded pdb=" O PHE P 846 " pdb=" OG SER P1040 " model vdw 2.247 2.440 nonbonded pdb=" NH1 ARG P 78 " pdb=" O ILE P 162 " model vdw 2.267 2.520 nonbonded pdb=" O VAL P 143 " pdb=" NE ARG P 425 " model vdw 2.270 2.520 nonbonded pdb=" OE1 GLU P1205 " pdb=" NH2 ARG P1359 " model vdw 2.275 2.520 ... (remaining 81196 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=1.00 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.960 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 36.020 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 55.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.009 0.294 10293 Z= 0.538 Angle : 1.080 10.446 14189 Z= 0.614 Chirality : 0.050 0.261 1605 Planarity : 0.007 0.073 1542 Dihedral : 18.189 160.859 4249 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % 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: -1.50 (0.23), residues: 1022 helix: -0.90 (0.20), residues: 514 sheet: -0.47 (0.48), residues: 104 loop : -1.03 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 883 HIS 0.017 0.002 HIS P1349 PHE 0.031 0.003 PHE P 405 TYR 0.016 0.002 TYR P 362 ARG 0.011 0.001 ARG P 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 10 ASP cc_start: 0.7147 (t70) cc_final: 0.6878 (t0) REVERT: P 781 MET cc_start: 0.7014 (tpp) cc_final: 0.6807 (tpp) outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 1.3243 time to fit residues: 333.0560 Evaluate side-chains 135 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1008 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 187 GLN P 190 GLN P 194 GLN ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 342 GLN P 726 ASN P 758 ASN P 771 GLN ** P 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10293 Z= 0.190 Angle : 0.554 6.960 14189 Z= 0.306 Chirality : 0.038 0.232 1605 Planarity : 0.004 0.031 1542 Dihedral : 19.699 146.412 2075 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.03 % Allowed : 15.23 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1022 helix: 0.25 (0.22), residues: 517 sheet: -0.17 (0.47), residues: 107 loop : -0.61 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P1074 HIS 0.004 0.001 HIS P 328 PHE 0.016 0.002 PHE P1008 TYR 0.019 0.001 TYR P 347 ARG 0.007 0.001 ARG P1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6398 (ttm-80) REVERT: P 281 GLN cc_start: 0.8270 (mp10) cc_final: 0.7968 (mp10) REVERT: P 763 MET cc_start: 0.7917 (mmt) cc_final: 0.7595 (mmt) REVERT: P 806 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7491 (mp) REVERT: P 1267 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6720 (t0) outliers start: 37 outliers final: 9 residues processed: 179 average time/residue: 1.2532 time to fit residues: 240.6552 Evaluate side-chains 134 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 194 GLN Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1267 ASP Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1332 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 160 HIS P 187 GLN P 194 GLN ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10293 Z= 0.207 Angle : 0.548 6.710 14189 Z= 0.302 Chirality : 0.038 0.207 1605 Planarity : 0.004 0.030 1542 Dihedral : 19.608 140.488 2073 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.24 % Allowed : 17.52 % Favored : 78.24 % 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 (0.25), residues: 1022 helix: 0.46 (0.23), residues: 505 sheet: 0.14 (0.47), residues: 106 loop : -0.47 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP P1074 HIS 0.006 0.001 HIS P 721 PHE 0.015 0.002 PHE P1276 TYR 0.019 0.002 TYR P 347 ARG 0.006 0.001 ARG P 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.6622 (ttm-80) REVERT: P 74 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7455 (mtp180) REVERT: P 163 LYS cc_start: 0.7418 (ttpt) cc_final: 0.7162 (ttmm) REVERT: P 402 GLN cc_start: 0.5368 (pm20) cc_final: 0.5037 (pp30) REVERT: P 806 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7602 (mp) REVERT: P 1071 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5413 (tp30) REVERT: P 1267 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6633 (t0) outliers start: 39 outliers final: 10 residues processed: 152 average time/residue: 1.2127 time to fit residues: 198.8639 Evaluate side-chains 131 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1267 ASP Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1332 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 11 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 160 HIS ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10293 Z= 0.191 Angle : 0.530 10.172 14189 Z= 0.287 Chirality : 0.037 0.141 1605 Planarity : 0.003 0.028 1542 Dihedral : 19.502 136.665 2073 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.81 % Allowed : 18.50 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1022 helix: 0.46 (0.23), residues: 513 sheet: 0.24 (0.48), residues: 104 loop : -0.61 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP P 883 HIS 0.005 0.001 HIS P 137 PHE 0.016 0.001 PHE P1276 TYR 0.019 0.002 TYR P 347 ARG 0.003 0.000 ARG P 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6752 (ttm-80) REVERT: P 83 GLN cc_start: 0.6591 (tp40) cc_final: 0.5319 (mt0) REVERT: P 163 LYS cc_start: 0.7420 (ttpt) cc_final: 0.7132 (ttmm) REVERT: P 197 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5839 (pm20) REVERT: P 251 ASN cc_start: 0.6537 (m-40) cc_final: 0.6326 (t0) REVERT: P 402 GLN cc_start: 0.5678 (pm20) cc_final: 0.5397 (pp30) REVERT: P 806 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7542 (mp) REVERT: P 1071 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5367 (tp30) REVERT: P 1219 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6753 (tt0) outliers start: 35 outliers final: 13 residues processed: 151 average time/residue: 1.1361 time to fit residues: 185.1908 Evaluate side-chains 132 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 270 THR Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 956 ILE Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1219 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1332 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 187 GLN P 194 GLN P 199 ASN ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 926 GLN ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1044 ASN P1221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10293 Z= 0.302 Angle : 0.619 9.313 14189 Z= 0.335 Chirality : 0.040 0.213 1605 Planarity : 0.004 0.031 1542 Dihedral : 19.765 135.553 2073 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.35 % Allowed : 19.48 % Favored : 76.17 % 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 (0.25), residues: 1022 helix: 0.25 (0.23), residues: 501 sheet: 0.40 (0.49), residues: 100 loop : -0.61 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP P1074 HIS 0.007 0.002 HIS P 721 PHE 0.021 0.002 PHE P 196 TYR 0.018 0.002 TYR P 25 ARG 0.004 0.001 ARG P 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7082 (ttm-80) REVERT: P 163 LYS cc_start: 0.7542 (ttpt) cc_final: 0.7263 (tttp) REVERT: P 197 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6106 (pm20) REVERT: P 402 GLN cc_start: 0.5810 (pm20) cc_final: 0.5495 (pp30) REVERT: P 795 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.6824 (pp) REVERT: P 806 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7622 (mp) REVERT: P 990 ASN cc_start: 0.7440 (m-40) cc_final: 0.7138 (m-40) REVERT: P 1071 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5234 (tp30) REVERT: P 1219 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6813 (tt0) outliers start: 40 outliers final: 14 residues processed: 153 average time/residue: 1.1851 time to fit residues: 195.3891 Evaluate side-chains 128 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 270 THR Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 795 ILE Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1219 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 0.0000 overall best weight: 0.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 194 GLN ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10293 Z= 0.162 Angle : 0.513 9.235 14189 Z= 0.281 Chirality : 0.037 0.167 1605 Planarity : 0.003 0.029 1542 Dihedral : 19.582 133.084 2073 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.83 % Allowed : 21.33 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1022 helix: 0.51 (0.23), residues: 501 sheet: 0.37 (0.49), residues: 100 loop : -0.49 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P1074 HIS 0.005 0.001 HIS P 137 PHE 0.013 0.001 PHE P1276 TYR 0.016 0.001 TYR P 347 ARG 0.002 0.000 ARG P 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.6971 (ttm-80) REVERT: P 163 LYS cc_start: 0.7511 (ttpt) cc_final: 0.7270 (ttmm) REVERT: P 402 GLN cc_start: 0.5811 (pm20) cc_final: 0.5499 (pp30) REVERT: P 806 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7612 (mp) REVERT: P 1071 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5438 (tp30) REVERT: P 1219 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6783 (tt0) outliers start: 26 outliers final: 13 residues processed: 132 average time/residue: 1.1812 time to fit residues: 168.2806 Evaluate side-chains 129 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 194 GLN Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1219 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1332 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10293 Z= 0.190 Angle : 0.540 8.725 14189 Z= 0.291 Chirality : 0.037 0.212 1605 Planarity : 0.003 0.031 1542 Dihedral : 19.503 130.891 2073 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.94 % Allowed : 22.74 % Favored : 74.32 % 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 (0.26), residues: 1022 helix: 0.57 (0.23), residues: 501 sheet: 0.58 (0.52), residues: 90 loop : -0.47 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P1074 HIS 0.005 0.001 HIS P 137 PHE 0.019 0.001 PHE P 196 TYR 0.014 0.001 TYR P 347 ARG 0.008 0.000 ARG P 783 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7005 (ttm-80) REVERT: P 163 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7253 (ttmm) REVERT: P 199 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7368 (m110) REVERT: P 251 ASN cc_start: 0.6671 (m-40) cc_final: 0.6382 (t0) REVERT: P 402 GLN cc_start: 0.5786 (pm20) cc_final: 0.5479 (pp30) REVERT: P 432 PHE cc_start: 0.5996 (OUTLIER) cc_final: 0.5588 (m-80) REVERT: P 806 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7666 (mp) REVERT: P 1071 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5468 (tp30) REVERT: P 1219 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: P 1242 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6380 (t80) outliers start: 27 outliers final: 9 residues processed: 131 average time/residue: 1.1495 time to fit residues: 163.2518 Evaluate side-chains 123 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 432 PHE Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1219 GLU Chi-restraints excluded: chain P residue 1242 TYR Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1332 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.0570 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 840 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10293 Z= 0.194 Angle : 0.542 8.370 14189 Z= 0.292 Chirality : 0.037 0.181 1605 Planarity : 0.003 0.030 1542 Dihedral : 19.459 129.410 2073 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.05 % Allowed : 22.52 % Favored : 74.43 % 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 (0.25), residues: 1022 helix: 0.65 (0.23), residues: 493 sheet: 0.61 (0.52), residues: 88 loop : -0.57 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P1074 HIS 0.004 0.001 HIS P 137 PHE 0.014 0.001 PHE P 196 TYR 0.014 0.001 TYR P 347 ARG 0.005 0.000 ARG P 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7050 (ttm-80) REVERT: P 402 GLN cc_start: 0.5788 (pm20) cc_final: 0.5482 (pp30) REVERT: P 806 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7624 (mp) REVERT: P 1071 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5485 (tp30) REVERT: P 1242 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.6367 (t80) outliers start: 28 outliers final: 12 residues processed: 124 average time/residue: 1.1863 time to fit residues: 158.9531 Evaluate side-chains 118 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 946 ASN Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1242 TYR Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1332 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.0040 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10293 Z= 0.199 Angle : 0.566 10.926 14189 Z= 0.302 Chirality : 0.038 0.228 1605 Planarity : 0.003 0.030 1542 Dihedral : 19.473 128.500 2073 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.50 % Allowed : 23.50 % Favored : 73.99 % 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: 0.15 (0.26), residues: 1022 helix: 0.70 (0.23), residues: 493 sheet: 0.54 (0.52), residues: 90 loop : -0.59 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 883 HIS 0.004 0.001 HIS P 137 PHE 0.016 0.001 PHE P1276 TYR 0.014 0.001 TYR P 25 ARG 0.004 0.000 ARG P 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7115 (ttm-80) REVERT: P 402 GLN cc_start: 0.5821 (pm20) cc_final: 0.5516 (pp30) REVERT: P 806 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7624 (mp) REVERT: P 1071 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5486 (tp30) REVERT: P 1242 TYR cc_start: 0.6700 (OUTLIER) cc_final: 0.6245 (t80) outliers start: 23 outliers final: 15 residues processed: 123 average time/residue: 1.1329 time to fit residues: 150.9417 Evaluate side-chains 118 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 161 MET Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 946 ASN Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1242 TYR Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1332 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.0270 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10293 Z= 0.225 Angle : 0.584 8.077 14189 Z= 0.312 Chirality : 0.039 0.195 1605 Planarity : 0.004 0.035 1542 Dihedral : 19.552 128.078 2073 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.61 % Allowed : 23.72 % Favored : 73.67 % 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: 0.01 (0.25), residues: 1022 helix: 0.55 (0.23), residues: 492 sheet: 0.46 (0.51), residues: 90 loop : -0.60 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 883 HIS 0.005 0.001 HIS P 328 PHE 0.016 0.002 PHE P1276 TYR 0.016 0.002 TYR P 25 ARG 0.009 0.001 ARG P 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7157 (ttm-80) REVERT: P 83 GLN cc_start: 0.6779 (tp40) cc_final: 0.6574 (tp40) REVERT: P 402 GLN cc_start: 0.5834 (pm20) cc_final: 0.5524 (pp30) REVERT: P 432 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: P 806 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7576 (mp) REVERT: P 1071 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5510 (tp30) REVERT: P 1242 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6361 (t80) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 1.0986 time to fit residues: 145.7780 Evaluate side-chains 126 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 270 THR Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 432 PHE Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 946 ASN Chi-restraints excluded: chain P residue 956 ILE Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1242 TYR Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1332 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 89 optimal weight: 0.0870 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.144095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.124396 restraints weight = 19494.890| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.49 r_work: 0.3855 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10293 Z= 0.176 Angle : 0.556 11.418 14189 Z= 0.296 Chirality : 0.037 0.190 1605 Planarity : 0.003 0.038 1542 Dihedral : 19.463 126.937 2073 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.39 % Allowed : 23.94 % Favored : 73.67 % 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: 0.13 (0.26), residues: 1022 helix: 0.69 (0.23), residues: 492 sheet: 0.51 (0.52), residues: 92 loop : -0.62 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 883 HIS 0.004 0.001 HIS P 167 PHE 0.011 0.001 PHE P1276 TYR 0.013 0.001 TYR P 347 ARG 0.009 0.000 ARG P 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3870.90 seconds wall clock time: 69 minutes 55.37 seconds (4195.37 seconds total)