Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 05:11:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/07_2023/7s36_24817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/07_2023/7s36_24817.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/07_2023/7s36_24817_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/07_2023/7s36_24817_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/07_2023/7s36_24817_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/07_2023/7s36_24817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/07_2023/7s36_24817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/07_2023/7s36_24817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/07_2023/7s36_24817_updated.pdb" } resolution = 3.2 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= 0.091 sd= 1.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 130 5.49 5 S 25 5.16 5 C 8311 2.51 5 N 2413 2.21 5 O 2942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 13821 Number of models: 1 Model: "" Number of chains: 4 Chain: "N" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 458 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "P" Number of atoms: 11065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 11065 Classifications: {'peptide': 1353} Link IDs: {'PTRANS': 35, 'TRANS': 1317} Chain breaks: 1 Chain: "R" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1854 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 41, 'rna3p_pyr': 34} Link IDs: {'rna2p': 12, 'rna3p': 74} Chain: "T" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 444 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 7.41, per 1000 atoms: 0.54 Number of scatterers: 13821 At special positions: 0 Unit cell: (123.9, 114.45, 107.1, 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 25 16.00 P 130 15.00 O 2942 8.00 N 2413 7.00 C 8311 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: 6.41 Conformation dependent library (CDL) restraints added in 1.9 seconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2574 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 8 sheets defined 46.9% alpha, 6.9% beta 42 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'P' and resid 60 through 93 removed outlier: 5.209A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'P' and resid 122 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 195 Processing helix chain 'P' and resid 208 through 212 Processing helix chain 'P' and resid 218 through 228 removed outlier: 3.578A pdb=" N GLN P 228 " --> pdb=" O ASN P 224 " (cutoff:3.500A) 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 305 removed outlier: 4.464A pdb=" N ASP P 288 " --> pdb=" O GLN P 285 " (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 390 through 394 Processing helix chain 'P' and resid 405 through 409 removed outlier: 3.766A 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 478 through 481 No H-bonds generated for 'chain 'P' and resid 478 through 481' Processing helix chain 'P' and resid 484 through 495 Processing helix chain 'P' and resid 513 through 526 removed outlier: 4.334A pdb=" N LYS P 526 " --> pdb=" O ASN P 522 " (cutoff:3.500A) Processing helix chain 'P' and resid 542 through 551 Processing helix chain 'P' and resid 561 through 567 Processing helix chain 'P' and resid 592 through 601 Processing helix chain 'P' and resid 604 through 608 removed outlier: 3.813A pdb=" N ASP P 608 " --> pdb=" O LYS P 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 604 through 608' Processing helix chain 'P' and resid 610 through 625 removed outlier: 3.783A pdb=" N GLU P 613 " --> pdb=" O GLU P 610 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP P 614 " --> pdb=" O GLU P 611 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL P 620 " --> pdb=" O GLU P 617 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU P 625 " --> pdb=" O THR P 622 " (cutoff:3.500A) Processing helix chain 'P' and resid 629 through 635 Processing helix chain 'P' and resid 647 through 653 Processing helix chain 'P' and resid 664 through 668 Processing helix chain 'P' and resid 679 through 684 Processing helix chain 'P' and resid 693 through 698 Processing helix chain 'P' and resid 703 through 710 Processing helix chain 'P' and resid 712 through 715 No H-bonds generated for 'chain 'P' and resid 712 through 715' Processing helix chain 'P' and resid 720 through 725 Processing helix chain 'P' and resid 731 through 750 Processing helix chain 'P' and resid 775 through 791 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: 3.551A 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: 3.790A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.581A 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 970 Processing helix chain 'P' and resid 981 through 1000 Processing helix chain 'P' and resid 1002 through 1008 removed outlier: 4.668A pdb=" N SER P1006 " --> pdb=" O LYS P1003 " (cutoff:3.500A) Processing helix chain 'P' and resid 1018 through 1021 No H-bonds generated for 'chain 'P' and resid 1018 through 1021' 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 1128 through 1131 No H-bonds generated for 'chain 'P' and resid 1128 through 1131' 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 1279 removed outlier: 3.509A pdb=" N GLU P1275 " --> pdb=" O GLN P1272 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE P1276 " --> pdb=" O ILE P1273 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS P1278 " --> pdb=" O GLU P1275 " (cutoff:3.500A) Processing helix chain 'P' and resid 1284 through 1296 Processing helix chain 'P' and resid 1302 through 1315 removed outlier: 3.623A pdb=" N HIS P1311 " --> pdb=" O GLU P1307 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR P1314 " --> pdb=" O ILE P1310 " (cutoff:3.500A) removed outlier: 4.635A 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 957 removed outlier: 6.424A pdb=" N ASN P1093 " --> pdb=" O ALA P 50 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU P 52 " --> pdb=" O ASN P1093 " (cutoff:3.500A) removed outlier: 6.190A 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: 7.042A pdb=" N GLU P1357 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.229A 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 1199 removed outlier: 7.150A pdb=" N ILE P1166 " --> pdb=" O ALA P1140 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER P1142 " --> pdb=" O LEU P1164 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU P1164 " --> pdb=" O SER P1142 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU P1144 " --> pdb=" O GLU P1162 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU P1162 " --> pdb=" O LEU P1144 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL P1146 " --> pdb=" O VAL P1160 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL P1160 " --> pdb=" O VAL P1146 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS P1148 " --> pdb=" O LYS P1158 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS P1158 " --> pdb=" O LYS P1148 " (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 405 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 7.53 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2198 1.32 - 1.45: 4299 1.45 - 1.57: 7531 1.57 - 1.69: 272 1.69 - 1.81: 46 Bond restraints: 14346 Sorted by residual: bond pdb=" C2' 2YR T 6 " pdb=" C3' 2YR T 6 " ideal model delta sigma weight residual 1.224 1.547 -0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C1' 2YR T 6 " pdb=" N1 2YR T 6 " ideal model delta sigma weight residual 1.348 1.519 -0.171 2.00e-02 2.50e+03 7.27e+01 bond pdb=" C4' 2YR T 6 " pdb=" O4' 2YR T 6 " ideal model delta sigma weight residual 1.271 1.440 -0.169 2.00e-02 2.50e+03 7.11e+01 bond pdb=" C5 2YR T 6 " pdb=" C6 2YR T 6 " ideal model delta sigma weight residual 1.499 1.340 0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C2 2YR T 6 " pdb=" N3 2YR T 6 " ideal model delta sigma weight residual 1.491 1.359 0.132 2.00e-02 2.50e+03 4.33e+01 ... (remaining 14341 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.48: 756 105.48 - 112.62: 7276 112.62 - 119.75: 5319 119.75 - 126.88: 6129 126.88 - 134.02: 434 Bond angle restraints: 19914 Sorted by residual: angle pdb=" CA GLU P 779 " pdb=" CB GLU P 779 " pdb=" CG GLU P 779 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 angle pdb=" C2' DT N 28 " pdb=" C1' DT N 28 " pdb=" N1 DT N 28 " ideal model delta sigma weight residual 113.50 119.31 -5.81 1.50e+00 4.44e-01 1.50e+01 angle pdb=" CB LYS P1096 " pdb=" CG LYS P1096 " pdb=" CD LYS P1096 " ideal model delta sigma weight residual 111.30 119.97 -8.67 2.30e+00 1.89e-01 1.42e+01 angle pdb=" O3' A R 42 " pdb=" C3' A R 42 " pdb=" C2' A R 42 " ideal model delta sigma weight residual 113.70 119.23 -5.53 1.50e+00 4.44e-01 1.36e+01 angle pdb=" C2' DT T 16 " pdb=" C1' DT T 16 " pdb=" N1 DT T 16 " ideal model delta sigma weight residual 113.50 119.02 -5.52 1.50e+00 4.44e-01 1.36e+01 ... (remaining 19909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 7894 25.98 - 51.96: 409 51.96 - 77.94: 93 77.94 - 103.93: 7 103.93 - 129.91: 2 Dihedral angle restraints: 8405 sinusoidal: 4425 harmonic: 3980 Sorted by residual: dihedral pdb=" CA ARG P1279 " pdb=" C ARG P1279 " pdb=" N VAL P1280 " pdb=" CA VAL P1280 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" C4' A R 42 " pdb=" C3' A R 42 " pdb=" O3' A R 42 " pdb=" P G R 43 " ideal model delta sinusoidal sigma weight residual 220.00 90.09 129.91 1 3.50e+01 8.16e-04 1.29e+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 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1945 0.066 - 0.131: 282 0.131 - 0.197: 40 0.197 - 0.262: 3 0.262 - 0.328: 1 Chirality restraints: 2271 Sorted by residual: chirality pdb=" C3' A R 46 " pdb=" C4' A R 46 " pdb=" O3' A R 46 " pdb=" C2' A R 46 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.69e+00 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 -2.62 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C3' A R 42 " pdb=" C4' A R 42 " pdb=" O3' A R 42 " pdb=" C2' A R 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2268 not shown) Planarity restraints: 2073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU P 302 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C LEU P 302 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU P 302 " 0.030 2.00e-02 2.50e+03 pdb=" N SER P 303 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A R 32 " 0.033 2.00e-02 2.50e+03 2.30e-02 1.46e+01 pdb=" N9 A R 32 " -0.063 2.00e-02 2.50e+03 pdb=" C8 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A R 32 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A R 32 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A R 32 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A R 32 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A R 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A R 32 " 0.028 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 3.79e-02 1.44e+01 pdb=" C ASP P 284 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP P 284 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN P 285 " 0.022 2.00e-02 2.50e+03 ... (remaining 2070 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1243 2.75 - 3.28: 13179 3.28 - 3.82: 23808 3.82 - 4.36: 29714 4.36 - 4.90: 46288 Nonbonded interactions: 114232 Sorted by model distance: nonbonded pdb=" O LEU P 101 " pdb=" O2' A R 47 " model vdw 2.207 2.440 nonbonded pdb=" NH2 ARG P 820 " pdb=" OD1 ASP P 825 " model vdw 2.252 2.520 nonbonded pdb=" NZ LYS P 742 " pdb=" OP1 C R 67 " model vdw 2.269 2.520 nonbonded pdb=" O LYS P 652 " pdb=" NH1 ARG P 655 " model vdw 2.279 2.520 nonbonded pdb=" ND2 ASN P 556 " pdb=" O LYS P 558 " model vdw 2.283 2.520 ... (remaining 114227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.640 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 44.940 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.008 0.323 14346 Z= 0.505 Angle : 0.987 9.921 19914 Z= 0.543 Chirality : 0.049 0.328 2271 Planarity : 0.006 0.046 2073 Dihedral : 15.126 129.907 5831 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.16 % 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 (0.20), residues: 1349 helix: -0.90 (0.17), residues: 655 sheet: -0.85 (0.46), residues: 125 loop : -0.94 (0.24), residues: 569 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 252 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.3643 time to fit residues: 123.3794 Evaluate side-chains 96 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1485 time to fit residues: 2.0541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.7980 chunk 111 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 133 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 690 ASN ** P 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14346 Z= 0.181 Angle : 0.543 9.508 19914 Z= 0.288 Chirality : 0.037 0.175 2271 Planarity : 0.003 0.035 2073 Dihedral : 15.832 133.551 2952 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1349 helix: 0.40 (0.20), residues: 652 sheet: -0.71 (0.45), residues: 128 loop : -0.56 (0.25), residues: 569 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 0.3173 time to fit residues: 47.7646 Evaluate side-chains 70 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1245 time to fit residues: 3.1044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 111 optimal weight: 0.0470 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 132 optimal weight: 0.0970 chunk 45 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.9078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 14346 Z= 0.170 Angle : 0.489 7.094 19914 Z= 0.262 Chirality : 0.036 0.261 2271 Planarity : 0.003 0.030 2073 Dihedral : 15.861 135.278 2952 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1349 helix: 0.77 (0.20), residues: 652 sheet: -0.66 (0.45), residues: 128 loop : -0.43 (0.25), residues: 569 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 93 average time/residue: 0.2802 time to fit residues: 38.8892 Evaluate side-chains 71 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1321 time to fit residues: 3.1572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.1980 chunk 100 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1027 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14346 Z= 0.153 Angle : 0.465 6.130 19914 Z= 0.250 Chirality : 0.035 0.177 2271 Planarity : 0.003 0.030 2073 Dihedral : 15.771 135.790 2952 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1349 helix: 0.94 (0.20), residues: 653 sheet: -0.63 (0.45), residues: 128 loop : -0.32 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 0.2776 time to fit residues: 35.6819 Evaluate side-chains 70 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 1.684 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1461 time to fit residues: 2.8705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14346 Z= 0.232 Angle : 0.497 6.906 19914 Z= 0.266 Chirality : 0.037 0.183 2271 Planarity : 0.003 0.029 2073 Dihedral : 15.885 136.064 2952 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1349 helix: 0.87 (0.20), residues: 653 sheet: -0.68 (0.45), residues: 128 loop : -0.29 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 80 average time/residue: 0.3143 time to fit residues: 37.0400 Evaluate side-chains 67 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1249 time to fit residues: 2.6598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14346 Z= 0.178 Angle : 0.479 7.343 19914 Z= 0.256 Chirality : 0.036 0.179 2271 Planarity : 0.003 0.029 2073 Dihedral : 15.862 135.846 2952 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1349 helix: 0.87 (0.20), residues: 654 sheet: -0.65 (0.45), residues: 128 loop : -0.21 (0.26), residues: 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 76 average time/residue: 0.2905 time to fit residues: 33.5991 Evaluate side-chains 68 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1482 time to fit residues: 2.5702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.6980 chunk 81 optimal weight: 0.2980 chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 88 optimal weight: 0.0470 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 758 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14346 Z= 0.148 Angle : 0.462 6.369 19914 Z= 0.248 Chirality : 0.036 0.178 2271 Planarity : 0.003 0.029 2073 Dihedral : 15.775 136.603 2952 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.23), residues: 1349 helix: 0.96 (0.20), residues: 659 sheet: -0.61 (0.45), residues: 128 loop : -0.18 (0.26), residues: 562 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 79 average time/residue: 0.2953 time to fit residues: 34.9480 Evaluate side-chains 69 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2833 time to fit residues: 2.7218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 0.0980 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 111 optimal weight: 0.0070 chunk 128 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 758 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14346 Z= 0.134 Angle : 0.452 6.706 19914 Z= 0.243 Chirality : 0.035 0.177 2271 Planarity : 0.003 0.029 2073 Dihedral : 15.689 137.105 2952 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1349 helix: 1.06 (0.21), residues: 659 sheet: -0.61 (0.44), residues: 130 loop : -0.20 (0.26), residues: 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.3045 time to fit residues: 32.1421 Evaluate side-chains 63 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1692 time to fit residues: 2.2515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 758 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 14346 Z= 0.254 Angle : 0.516 9.439 19914 Z= 0.273 Chirality : 0.038 0.184 2271 Planarity : 0.003 0.028 2073 Dihedral : 15.794 136.567 2952 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1349 helix: 0.96 (0.20), residues: 658 sheet: -0.65 (0.44), residues: 131 loop : -0.24 (0.26), residues: 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.3014 time to fit residues: 31.8921 Evaluate side-chains 64 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1308 time to fit residues: 2.2123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 14346 Z= 0.190 Angle : 0.484 9.996 19914 Z= 0.258 Chirality : 0.036 0.179 2271 Planarity : 0.003 0.028 2073 Dihedral : 15.771 135.634 2952 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1349 helix: 0.92 (0.20), residues: 659 sheet: -0.71 (0.44), residues: 130 loop : -0.26 (0.26), residues: 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2947 time to fit residues: 28.2154 Evaluate side-chains 61 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.0570 chunk 48 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 709 GLN P 758 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.104688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076177 restraints weight = 29475.467| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.19 r_work: 0.3040 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 14346 Z= 0.127 Angle : 0.447 8.990 19914 Z= 0.240 Chirality : 0.035 0.174 2271 Planarity : 0.003 0.028 2073 Dihedral : 15.614 136.523 2952 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1349 helix: 1.05 (0.21), residues: 659 sheet: -0.45 (0.44), residues: 129 loop : -0.24 (0.26), residues: 561 =============================================================================== Job complete usr+sys time: 2557.40 seconds wall clock time: 48 minutes 28.60 seconds (2908.60 seconds total)