Starting phenix.real_space_refine on Sat Dec 9 03:35:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2023/7s3h_24823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2023/7s3h_24823.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2023/7s3h_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_24823/12_2023/7s3h_24823_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2023/7s3h_24823_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2023/7s3h_24823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2023/7s3h_24823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2023/7s3h_24823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2023/7s3h_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.21, per 1000 atoms: 0.62 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: 4.88 Conformation dependent library (CDL) restraints added in 1.5 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: 5.19 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: 4.76 Time building geometry restraints manager: 5.14 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: 0.840 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: 3.920 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 36.040 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.770 ------------------------------------------------------------------------------- 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 : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 1.3369 time to fit residues: 336.0402 Evaluate side-chains 135 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 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: 0.7138 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10293 Z= 0.206 Angle : 0.568 7.055 14189 Z= 0.312 Chirality : 0.038 0.235 1605 Planarity : 0.004 0.030 1542 Dihedral : 19.664 145.834 2073 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.13 % Allowed : 15.45 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1022 helix: 0.26 (0.22), residues: 515 sheet: -0.05 (0.49), residues: 100 loop : -0.62 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P1074 HIS 0.004 0.001 HIS P 328 PHE 0.011 0.002 PHE P1008 TYR 0.020 0.001 TYR P 347 ARG 0.008 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 191 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 10 residues processed: 177 average time/residue: 1.2445 time to fit residues: 236.2922 Evaluate side-chains 133 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 1.0946 time to fit residues: 3.8124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3194 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= 0.194 Angle : 0.542 10.121 14189 Z= 0.296 Chirality : 0.038 0.192 1605 Planarity : 0.003 0.030 1542 Dihedral : 19.595 140.419 2073 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.92 % Allowed : 17.19 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1022 helix: 0.50 (0.23), residues: 503 sheet: 0.14 (0.47), residues: 106 loop : -0.59 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP P1074 HIS 0.005 0.001 HIS P 721 PHE 0.014 0.001 PHE P 432 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 164 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 14 residues processed: 149 average time/residue: 1.0991 time to fit residues: 177.1221 Evaluate side-chains 125 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.4396 time to fit residues: 3.0079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10293 Z= 0.226 Angle : 0.557 8.522 14189 Z= 0.302 Chirality : 0.038 0.141 1605 Planarity : 0.004 0.037 1542 Dihedral : 19.581 136.824 2073 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.81 % Allowed : 18.61 % Favored : 77.58 % 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: -0.10 (0.25), residues: 1022 helix: 0.39 (0.23), residues: 512 sheet: 0.32 (0.48), residues: 104 loop : -0.62 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P1074 HIS 0.007 0.001 HIS P 137 PHE 0.017 0.002 PHE P1276 TYR 0.018 0.002 TYR P 347 ARG 0.004 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 159 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 1.116 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 146 average time/residue: 1.0971 time to fit residues: 173.5916 Evaluate side-chains 128 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.3105 time to fit residues: 3.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 187 GLN ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10293 Z= 0.224 Angle : 0.551 7.706 14189 Z= 0.300 Chirality : 0.038 0.151 1605 Planarity : 0.004 0.028 1542 Dihedral : 19.618 135.367 2073 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.24 % Allowed : 19.37 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1022 helix: 0.44 (0.23), residues: 505 sheet: 0.32 (0.49), residues: 102 loop : -0.66 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 883 HIS 0.009 0.001 HIS P 137 PHE 0.017 0.002 PHE P 196 TYR 0.016 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 157 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.202 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 17 residues processed: 146 average time/residue: 1.1548 time to fit residues: 182.3812 Evaluate side-chains 122 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.1494 time to fit residues: 2.4335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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** ** P 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4237 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= 0.194 Angle : 0.543 7.793 14189 Z= 0.294 Chirality : 0.037 0.166 1605 Planarity : 0.004 0.049 1542 Dihedral : 19.580 133.140 2073 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.26 % Allowed : 21.44 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1022 helix: 0.51 (0.23), residues: 504 sheet: 0.33 (0.49), residues: 102 loop : -0.57 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P1074 HIS 0.007 0.001 HIS P 137 PHE 0.015 0.001 PHE P1276 TYR 0.016 0.001 TYR P 347 ARG 0.003 0.000 ARG P 905 *********************** 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 144 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 134 average time/residue: 1.2104 time to fit residues: 175.2609 Evaluate side-chains 129 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.1404 time to fit residues: 2.3202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 187 GLN ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1044 ASN P1221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10293 Z= 0.250 Angle : 0.591 7.225 14189 Z= 0.317 Chirality : 0.039 0.209 1605 Planarity : 0.004 0.035 1542 Dihedral : 19.634 131.578 2073 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.37 % Allowed : 21.55 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1022 helix: 0.41 (0.23), residues: 503 sheet: 0.60 (0.51), residues: 90 loop : -0.62 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 18 HIS 0.006 0.001 HIS P 137 PHE 0.019 0.002 PHE P 196 TYR 0.018 0.002 TYR P 25 ARG 0.004 0.001 ARG P 307 *********************** 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 150 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.107 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 137 average time/residue: 1.1703 time to fit residues: 173.3076 Evaluate side-chains 132 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.6931 time to fit residues: 6.1071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4630 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= 0.221 Angle : 0.582 10.125 14189 Z= 0.312 Chirality : 0.038 0.186 1605 Planarity : 0.004 0.033 1542 Dihedral : 19.576 130.212 2073 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.50 % Allowed : 22.96 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1022 helix: 0.44 (0.23), residues: 502 sheet: 0.48 (0.51), residues: 90 loop : -0.68 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P1074 HIS 0.005 0.001 HIS P 328 PHE 0.015 0.002 PHE P 196 TYR 0.015 0.002 TYR P 25 ARG 0.012 0.001 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 132 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 1.0906 time to fit residues: 150.7813 Evaluate side-chains 123 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1575 time to fit residues: 2.2259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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** P 754 HIS ** P 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 990 ASN ** 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: 0.7281 moved from start: 0.4671 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= 0.180 Angle : 0.546 7.411 14189 Z= 0.295 Chirality : 0.037 0.241 1605 Planarity : 0.003 0.033 1542 Dihedral : 19.492 128.781 2073 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.29 % Allowed : 23.83 % Favored : 73.88 % 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: 0.04 (0.26), residues: 1022 helix: 0.57 (0.23), residues: 502 sheet: 0.50 (0.51), residues: 90 loop : -0.62 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 18 HIS 0.004 0.001 HIS P 328 PHE 0.012 0.001 PHE P1276 TYR 0.014 0.001 TYR P 347 ARG 0.011 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 129 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.048 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 123 average time/residue: 1.1187 time to fit residues: 149.5524 Evaluate side-chains 117 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1691 time to fit residues: 2.2409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 926 GLN ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10293 Z= 0.212 Angle : 0.583 11.076 14189 Z= 0.310 Chirality : 0.038 0.239 1605 Planarity : 0.004 0.032 1542 Dihedral : 19.550 128.031 2073 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.85 % Allowed : 24.37 % Favored : 73.78 % 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: -0.08 (0.25), residues: 1022 helix: 0.49 (0.23), residues: 501 sheet: 0.42 (0.50), residues: 90 loop : -0.70 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 883 HIS 0.004 0.001 HIS P 328 PHE 0.016 0.001 PHE P1276 TYR 0.014 0.002 TYR P 25 ARG 0.011 0.001 ARG P 139 ********************** 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 124 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.163 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 1.0728 time to fit residues: 140.3001 Evaluate side-chains 113 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.4871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** ** P 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 GLN ** 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 = 0.4172 r_free = 0.4172 target = 0.140502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.120728 restraints weight = 19233.823| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.47 r_work: 0.3799 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10293 Z= 0.283 Angle : 0.649 10.804 14189 Z= 0.345 Chirality : 0.041 0.231 1605 Planarity : 0.004 0.034 1542 Dihedral : 19.721 128.175 2073 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.96 % Allowed : 24.27 % Favored : 73.78 % 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: -0.38 (0.25), residues: 1022 helix: 0.23 (0.23), residues: 499 sheet: 0.27 (0.50), residues: 90 loop : -0.82 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP P1074 HIS 0.006 0.001 HIS P 328 PHE 0.021 0.002 PHE P 196 TYR 0.019 0.002 TYR P 25 ARG 0.013 0.001 ARG P 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3840.98 seconds wall clock time: 69 minutes 14.62 seconds (4154.62 seconds total)