Starting phenix.real_space_refine (version: dev) on Sun Feb 19 11:23:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/02_2023/7s3h_24823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/02_2023/7s3h_24823.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/02_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_24823/02_2023/7s3h_24823_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/02_2023/7s3h_24823_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/02_2023/7s3h_24823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/02_2023/7s3h_24823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/02_2023/7s3h_24823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s3h_24823/02_2023/7s3h_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 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-dev-4877/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: 6.08, per 1000 atoms: 0.61 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: 4.70 Conformation dependent library (CDL) restraints added in 1.3 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: 3.75 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: 4.43 Time building geometry restraints manager: 4.86 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 - 17.26: 5287 17.26 - 34.51: 471 34.51 - 51.77: 220 51.77 - 69.02: 82 69.02 - 86.28: 9 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 - 0.052: 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 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: 1.230 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: 4.320 Check model and map are aligned: 0.150 Process input model: 32.910 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.490 ------------------------------------------------------------------------------- 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 0.294 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 : 16.857 86.276 4109 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 % 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 : 1.040 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: 1.3479 time to fit residues: 339.2365 Evaluate side-chains 135 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4869 ------------------------------------------------------------------------------- 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 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 342 GLN P 726 ASN P 758 ASN P 771 GLN ** P 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2473 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= 0.204 Angle : 0.564 7.022 14189 Z= 0.310 Chirality : 0.038 0.227 1605 Planarity : 0.004 0.033 1542 Dihedral : 17.637 83.928 1933 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 4.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1022 helix: 0.27 (0.22), residues: 515 sheet: -0.05 (0.49), residues: 100 loop : -0.62 (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 194 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 10 residues processed: 179 average time/residue: 1.2392 time to fit residues: 238.1581 Evaluate side-chains 132 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.8274 time to fit residues: 3.3057 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7404 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10293 Z= 0.216 Angle : 0.562 10.211 14189 Z= 0.307 Chirality : 0.038 0.194 1605 Planarity : 0.004 0.028 1542 Dihedral : 17.572 88.001 1933 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 4.35 % 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: 0.42 (0.23), residues: 504 sheet: 0.27 (0.49), residues: 94 loop : -0.60 (0.28), residues: 424 *********************** 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 170 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.099 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 155 average time/residue: 1.2497 time to fit residues: 208.8148 Evaluate side-chains 127 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.1463 time to fit residues: 2.3459 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 0.1980 chunk 11 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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: 0.7383 moved from start: 0.3612 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= 0.166 Angle : 0.511 8.571 14189 Z= 0.279 Chirality : 0.036 0.142 1605 Planarity : 0.003 0.029 1542 Dihedral : 17.395 86.398 1933 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 3.70 % 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: 0.50 (0.23), residues: 514 sheet: 0.28 (0.48), residues: 104 loop : -0.58 (0.29), residues: 404 *********************** 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 154 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 146 average time/residue: 1.1581 time to fit residues: 182.9417 Evaluate side-chains 124 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.0944 time to fit residues: 1.5826 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 83 GLN P 187 GLN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10293 Z= 0.215 Angle : 0.544 7.755 14189 Z= 0.296 Chirality : 0.038 0.191 1605 Planarity : 0.003 0.027 1542 Dihedral : 17.483 89.193 1933 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -0.10 (0.25), residues: 1022 helix: 0.44 (0.23), residues: 510 sheet: 0.32 (0.48), residues: 102 loop : -0.70 (0.29), residues: 410 *********************** 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 160 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 147 average time/residue: 1.1631 time to fit residues: 185.8441 Evaluate side-chains 127 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1561 time to fit residues: 2.6872 ------------------------------------------------------------------------------- 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: 0.0030 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.0010 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10293 Z= 0.160 Angle : 0.528 9.195 14189 Z= 0.287 Chirality : 0.037 0.169 1605 Planarity : 0.003 0.029 1542 Dihedral : 17.383 86.096 1933 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -0.00 (0.25), residues: 1022 helix: 0.52 (0.23), residues: 509 sheet: 0.36 (0.49), residues: 104 loop : -0.64 (0.29), residues: 409 *********************** 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 152 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 142 average time/residue: 1.1704 time to fit residues: 180.4248 Evaluate side-chains 128 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.1744 time to fit residues: 2.2612 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ** P1044 ASN ** 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: 0.7432 moved from start: 0.4332 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= 0.192 Angle : 0.549 9.114 14189 Z= 0.297 Chirality : 0.037 0.175 1605 Planarity : 0.004 0.057 1542 Dihedral : 17.400 88.133 1933 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -0.04 (0.25), residues: 1022 helix: 0.49 (0.23), residues: 509 sheet: 0.53 (0.51), residues: 92 loop : -0.68 (0.29), residues: 421 *********************** 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 141 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 135 average time/residue: 1.0640 time to fit residues: 156.3483 Evaluate side-chains 126 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1726 time to fit residues: 2.4138 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 ** 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: 0.7406 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10293 Z= 0.173 Angle : 0.537 7.729 14189 Z= 0.288 Chirality : 0.037 0.217 1605 Planarity : 0.003 0.051 1542 Dihedral : 17.359 86.534 1933 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 2.50 % 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 (0.26), residues: 1022 helix: 0.58 (0.23), residues: 507 sheet: 0.39 (0.51), residues: 95 loop : -0.71 (0.29), residues: 420 *********************** 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 137 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 132 average time/residue: 1.0050 time to fit residues: 144.5468 Evaluate side-chains 123 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.1335 time to fit residues: 1.5245 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.0170 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 ** 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: 0.7405 moved from start: 0.4510 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= 0.177 Angle : 0.553 10.699 14189 Z= 0.295 Chirality : 0.038 0.196 1605 Planarity : 0.003 0.029 1542 Dihedral : 17.380 86.698 1933 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: -0.02 (0.26), residues: 1022 helix: 0.52 (0.23), residues: 505 sheet: 0.42 (0.51), residues: 95 loop : -0.66 (0.29), residues: 422 *********************** 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 136 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.986 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 129 average time/residue: 1.1381 time to fit residues: 160.5159 Evaluate side-chains 118 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.1703 time to fit residues: 2.5445 ------------------------------------------------------------------------------- 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: 0.6980 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** P1044 ASN ** 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: 0.7425 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10293 Z= 0.195 Angle : 0.571 10.404 14189 Z= 0.303 Chirality : 0.038 0.192 1605 Planarity : 0.003 0.035 1542 Dihedral : 17.386 87.688 1933 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -0.07 (0.26), residues: 1022 helix: 0.49 (0.23), residues: 508 sheet: 0.43 (0.50), residues: 94 loop : -0.71 (0.29), residues: 420 ********************** 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 127 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 120 average time/residue: 1.1505 time to fit residues: 150.6718 Evaluate side-chains 116 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2686 time to fit residues: 1.9075 ------------------------------------------------------------------------------- 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: 2.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.144227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.124271 restraints weight = 19480.961| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.50 r_work: 0.3849 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10293 Z= 0.206 Angle : 0.574 9.072 14189 Z= 0.305 Chirality : 0.038 0.187 1605 Planarity : 0.003 0.033 1542 Dihedral : 17.423 88.187 1933 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 2.07 % 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 (0.26), residues: 1022 helix: 0.50 (0.23), residues: 504 sheet: 0.43 (0.50), residues: 92 loop : -0.76 (0.29), residues: 426 =============================================================================== Job complete usr+sys time: 3805.30 seconds wall clock time: 68 minutes 46.95 seconds (4126.95 seconds total)