Starting phenix.real_space_refine (version: dev) on Mon Dec 12 10:01:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2022/7s3h_24823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2022/7s3h_24823.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2022/7s3h_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_2022/7s3h_24823_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2022/7s3h_24823_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2022/7s3h_24823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2022/7s3h_24823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2022/7s3h_24823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/12_2022/7s3h_24823_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4807/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: 6.50, per 1000 atoms: 0.65 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: 4.92 Conformation dependent library (CDL) restraints added in 1.1 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: 4.37 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: 5.08 Time building geometry restraints manager: 5.09 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 1.221 1.518 -0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C4' 2YR T 6 " pdb=" O4' 2YR T 6 " ideal model delta sigma weight residual 1.269 1.465 -0.196 2.00e-02 2.50e+03 9.60e+01 bond pdb=" C1' 2YR T 6 " pdb=" N1 2YR T 6 " ideal model delta sigma weight residual 1.343 1.527 -0.184 2.00e-02 2.50e+03 8.43e+01 bond pdb=" C5 2YR T 6 " pdb=" C6 2YR T 6 " ideal model delta sigma weight residual 1.495 1.336 0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" C2 2YR T 6 " pdb=" N3 2YR T 6 " ideal model delta sigma weight residual 1.489 1.360 0.129 2.00e-02 2.50e+03 4.17e+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 - 17.26: 5286 17.26 - 34.51: 470 34.51 - 51.77: 221 51.77 - 69.02: 82 69.02 - 86.28: 10 Dihedral angle restraints: 6069 sinusoidal: 3039 harmonic: 3030 Sorted by residual: 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 dihedral pdb=" CA ASP P 912 " pdb=" CB ASP P 912 " pdb=" CG ASP P 912 " pdb=" OD1 ASP P 912 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 6066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1188 0.053 - 0.105: 340 0.105 - 0.158: 67 0.158 - 0.210: 7 0.210 - 0.263: 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 1.73e+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 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. 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: 4.160 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 34.740 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 0.297 10293 Z= 0.538 Angle : 1.080 10.436 14189 Z= 0.614 Chirality : 0.050 0.263 1605 Planarity : 0.007 0.073 1542 Dihedral : 16.905 86.276 4109 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.11 % 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 *********************** 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 : 1.066 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: 1.2330 time to fit residues: 311.4036 Evaluate side-chains 135 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4873 ------------------------------------------------------------------------------- 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: 0.7311 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10293 Z= 0.205 Angle : 0.565 6.947 14189 Z= 0.311 Chirality : 0.038 0.254 1605 Planarity : 0.004 0.031 1542 Dihedral : 17.751 84.173 1933 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 4.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1022 helix: 0.26 (0.22), residues: 515 sheet: -0.06 (0.49), residues: 100 loop : -0.63 (0.29), residues: 407 *********************** 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 : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 10 residues processed: 178 average time/residue: 1.1769 time to fit residues: 225.6535 Evaluate side-chains 133 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 1.1152 time to fit residues: 3.8408 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 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: 0.0770 chunk 80 optimal weight: 3.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3556 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= 0.279 Angle : 0.616 6.977 14189 Z= 0.337 Chirality : 0.040 0.213 1605 Planarity : 0.004 0.030 1542 Dihedral : 17.816 90.760 1933 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 4.90 % 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: -0.11 (0.25), residues: 1022 helix: 0.33 (0.23), residues: 495 sheet: 0.38 (0.50), residues: 92 loop : -0.51 (0.28), residues: 435 *********************** 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 173 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.108 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 15 residues processed: 156 average time/residue: 1.1196 time to fit residues: 189.1122 Evaluate side-chains 121 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1589 time to fit residues: 2.1571 ------------------------------------------------------------------------------- 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: 3.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.0040 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.4972 ------------------------------------------------------------------------------- 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** ** P1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3798 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= 0.168 Angle : 0.528 10.500 14189 Z= 0.287 Chirality : 0.037 0.165 1605 Planarity : 0.003 0.030 1542 Dihedral : 17.565 87.081 1933 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 3.81 % 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: 0.42 (0.23), residues: 507 sheet: 0.23 (0.48), residues: 104 loop : -0.55 (0.29), residues: 411 *********************** 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 152 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 142 average time/residue: 1.1183 time to fit residues: 172.3360 Evaluate side-chains 129 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.4195 time to fit residues: 3.5332 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** P 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 990 ASN ** 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: 0.7490 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10293 Z= 0.261 Angle : 0.591 8.992 14189 Z= 0.319 Chirality : 0.040 0.238 1605 Planarity : 0.004 0.045 1542 Dihedral : 17.722 90.883 1933 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 3.92 % 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: -0.22 (0.25), residues: 1022 helix: 0.24 (0.23), residues: 509 sheet: 0.36 (0.48), residues: 100 loop : -0.62 (0.29), residues: 413 *********************** 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 155 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 144 average time/residue: 1.0812 time to fit residues: 169.8236 Evaluate side-chains 129 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.5026 time to fit residues: 3.9306 ------------------------------------------------------------------------------- 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: 0.2980 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.0370 chunk 55 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 160 HIS ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1044 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: 0.7405 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 10293 Z= 0.153 Angle : 0.513 9.223 14189 Z= 0.279 Chirality : 0.037 0.173 1605 Planarity : 0.003 0.036 1542 Dihedral : 17.534 85.793 1933 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1022 helix: 0.51 (0.23), residues: 504 sheet: 0.39 (0.48), residues: 104 loop : -0.55 (0.30), residues: 414 *********************** 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 145 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 136 average time/residue: 1.1277 time to fit residues: 166.5021 Evaluate side-chains 120 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1621 time to fit residues: 2.3378 ------------------------------------------------------------------------------- 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: 0.5980 chunk 77 optimal weight: 0.0870 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** ** 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: 0.7434 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 10293 Z= 0.182 Angle : 0.557 9.579 14189 Z= 0.298 Chirality : 0.038 0.278 1605 Planarity : 0.003 0.031 1542 Dihedral : 17.511 87.142 1933 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 2.61 % 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: 0.48 (0.23), residues: 499 sheet: 0.51 (0.51), residues: 92 loop : -0.56 (0.29), residues: 431 *********************** 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 136 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 130 average time/residue: 1.0516 time to fit residues: 149.0333 Evaluate side-chains 123 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1641 time to fit residues: 2.2090 ------------------------------------------------------------------------------- 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: 0.5980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 96 optimal weight: 0.0170 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 840 HIS P1044 ASN ** P1221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4557 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= 0.194 Angle : 0.563 8.851 14189 Z= 0.303 Chirality : 0.039 0.229 1605 Planarity : 0.003 0.040 1542 Dihedral : 17.501 87.561 1933 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 2.94 % 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: 498 sheet: 0.65 (0.51), residues: 88 loop : -0.55 (0.29), residues: 436 *********************** 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 133 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 127 average time/residue: 1.0358 time to fit residues: 144.0917 Evaluate side-chains 120 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1583 time to fit residues: 2.4535 ------------------------------------------------------------------------------- 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: 4.9990 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.0970 chunk 64 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** ** P1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10293 Z= 0.188 Angle : 0.572 10.066 14189 Z= 0.303 Chirality : 0.039 0.248 1605 Planarity : 0.003 0.030 1542 Dihedral : 17.508 87.250 1933 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 2.18 % 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: 0.43 (0.23), residues: 498 sheet: 0.63 (0.51), residues: 88 loop : -0.54 (0.29), residues: 436 *********************** 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: 20 poor density : 112 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 128 average time/residue: 1.0522 time to fit residues: 146.8093 Evaluate side-chains 123 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1845 time to fit residues: 1.9991 ------------------------------------------------------------------------------- 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: 0.5980 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** P 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10293 Z= 0.193 Angle : 0.576 10.206 14189 Z= 0.306 Chirality : 0.039 0.252 1605 Planarity : 0.003 0.038 1542 Dihedral : 17.516 87.097 1933 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 2.39 % 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: -0.04 (0.25), residues: 1022 helix: 0.44 (0.23), residues: 498 sheet: 0.62 (0.52), residues: 88 loop : -0.59 (0.29), residues: 436 ********************** 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 125 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.099 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 119 average time/residue: 1.1004 time to fit residues: 142.5776 Evaluate side-chains 116 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.2035 time to fit residues: 2.4826 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1261 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 = 0.4220 r_free = 0.4220 target = 0.144387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.124620 restraints weight = 19513.696| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.53 r_work: 0.3852 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 10293 Z= 0.192 Angle : 0.576 10.729 14189 Z= 0.303 Chirality : 0.039 0.243 1605 Planarity : 0.003 0.033 1542 Dihedral : 17.525 87.157 1933 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 2.39 % 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: -0.02 (0.26), residues: 1022 helix: 0.49 (0.23), residues: 500 sheet: 0.53 (0.51), residues: 90 loop : -0.62 (0.29), residues: 432 =============================================================================== Job complete usr+sys time: 3707.74 seconds wall clock time: 66 minutes 40.83 seconds (4000.83 seconds total)