Starting phenix.real_space_refine on Fri Feb 16 00:20:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/02_2024/7s36_24817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/02_2024/7s36_24817.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/02_2024/7s36_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_24817/02_2024/7s36_24817_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/02_2024/7s36_24817_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/02_2024/7s36_24817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/02_2024/7s36_24817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/02_2024/7s36_24817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s36_24817/02_2024/7s36_24817_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.091 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.49, 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: 6.38 Conformation dependent library (CDL) restraints added in 2.3 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: 7.62 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: 6.99 Time building geometry restraints manager: 6.75 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 - 28.84: 8127 28.84 - 57.69: 497 57.69 - 86.53: 115 86.53 - 115.37: 1 115.37 - 144.21: 3 Dihedral angle restraints: 8743 sinusoidal: 4763 harmonic: 3980 Sorted by residual: dihedral pdb=" C3' 2YR T 6 " pdb=" C4' 2YR T 6 " pdb=" C5' 2YR T 6 " pdb=" O5' 2YR T 6 " ideal model delta sinusoidal sigma weight residual 191.74 47.53 144.21 1 3.00e+01 1.11e-03 1.93e+01 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 ... (remaining 8740 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: 0.930 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: 4.080 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 46.070 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.820 ------------------------------------------------------------------------------- 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 : 17.426 144.214 6169 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 % Allowed : 3.95 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 476 HIS 0.010 0.002 HIS P 116 PHE 0.026 0.003 PHE P 405 TYR 0.021 0.002 TYR P 812 ARG 0.008 0.001 ARG P 66 *********************** 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 : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8311 (mt) cc_final: 0.8101 (mp) REVERT: P 338 LEU cc_start: 0.9035 (mt) cc_final: 0.8753 (mp) REVERT: P 816 LEU cc_start: 0.8846 (mt) cc_final: 0.8288 (mt) REVERT: P 822 MET cc_start: 0.8273 (mmp) cc_final: 0.7904 (tpp) REVERT: P 841 ILE cc_start: 0.8985 (mm) cc_final: 0.8747 (mp) REVERT: P 930 HIS cc_start: 0.7620 (m90) cc_final: 0.7208 (m90) REVERT: P 1037 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7623 (p90) REVERT: P 1180 ASP cc_start: 0.7305 (m-30) cc_final: 0.7094 (m-30) outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.3714 time to fit residues: 126.9942 Evaluate side-chains 98 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1037 PHE 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: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.8141 moved from start: 0.2115 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= 0.207 Angle : 0.544 8.686 19914 Z= 0.291 Chirality : 0.038 0.179 2271 Planarity : 0.004 0.032 2073 Dihedral : 19.574 147.001 3294 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.99 % Allowed : 10.04 % Favored : 88.97 % 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: -0.23 (0.22), residues: 1349 helix: 0.42 (0.20), residues: 652 sheet: -0.73 (0.45), residues: 128 loop : -0.55 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 476 HIS 0.006 0.001 HIS P 116 PHE 0.012 0.001 PHE P 643 TYR 0.013 0.001 TYR P 155 ARG 0.004 0.001 ARG P1122 *********************** 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 110 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8427 (mt) cc_final: 0.8193 (mp) REVERT: P 534 MET cc_start: 0.7620 (mmm) cc_final: 0.6371 (ptt) REVERT: P 649 LYS cc_start: 0.8353 (tmtt) cc_final: 0.8079 (mtmm) REVERT: P 694 MET cc_start: 0.7795 (tpp) cc_final: 0.7544 (tpp) REVERT: P 781 MET cc_start: 0.8032 (mmm) cc_final: 0.7231 (mmm) REVERT: P 816 LEU cc_start: 0.8999 (mt) cc_final: 0.8451 (mt) REVERT: P 930 HIS cc_start: 0.7545 (m90) cc_final: 0.7146 (m90) REVERT: P 1037 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7707 (p90) outliers start: 12 outliers final: 6 residues processed: 108 average time/residue: 0.3042 time to fit residues: 47.1561 Evaluate side-chains 79 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 95 ASP Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1072 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14346 Z= 0.300 Angle : 0.562 7.068 19914 Z= 0.299 Chirality : 0.039 0.189 2271 Planarity : 0.004 0.034 2073 Dihedral : 19.772 154.165 3292 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 10.62 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1349 helix: 0.55 (0.20), residues: 651 sheet: -0.87 (0.44), residues: 128 loop : -0.36 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 476 HIS 0.006 0.001 HIS P 116 PHE 0.015 0.002 PHE P1008 TYR 0.014 0.002 TYR P 155 ARG 0.010 0.001 ARG P 832 *********************** 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 102 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 90 MET cc_start: 0.8665 (tpp) cc_final: 0.8209 (tpt) REVERT: P 216 LEU cc_start: 0.8546 (mt) cc_final: 0.8297 (mp) REVERT: P 534 MET cc_start: 0.7572 (mmm) cc_final: 0.6364 (ptt) REVERT: P 649 LYS cc_start: 0.8331 (tmtt) cc_final: 0.8062 (mtmm) REVERT: P 930 HIS cc_start: 0.7565 (m90) cc_final: 0.6936 (m90) REVERT: P 1037 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7802 (p90) outliers start: 22 outliers final: 11 residues processed: 99 average time/residue: 0.2996 time to fit residues: 43.3179 Evaluate side-chains 80 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 95 ASP Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 597 LEU Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 758 ASN P1027 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14346 Z= 0.193 Angle : 0.487 6.781 19914 Z= 0.262 Chirality : 0.037 0.183 2271 Planarity : 0.003 0.030 2073 Dihedral : 19.724 163.469 3292 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.65 % Allowed : 10.62 % Favored : 87.74 % 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: 0.19 (0.23), residues: 1349 helix: 0.77 (0.20), residues: 650 sheet: -0.82 (0.45), residues: 128 loop : -0.26 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 476 HIS 0.004 0.001 HIS P 116 PHE 0.014 0.001 PHE P1008 TYR 0.015 0.001 TYR P1016 ARG 0.004 0.000 ARG P 832 *********************** 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 96 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8513 (mt) cc_final: 0.8282 (mp) REVERT: P 534 MET cc_start: 0.7577 (mmm) cc_final: 0.6268 (ptt) REVERT: P 789 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8798 (mmmt) REVERT: P 912 ASP cc_start: 0.7152 (m-30) cc_final: 0.6808 (m-30) REVERT: P 930 HIS cc_start: 0.7591 (m90) cc_final: 0.6903 (m90) REVERT: P 1037 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7918 (p90) outliers start: 20 outliers final: 10 residues processed: 94 average time/residue: 0.2885 time to fit residues: 40.0582 Evaluate side-chains 75 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 597 LEU Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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: 0.8211 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 0.036 14346 Z= 0.190 Angle : 0.480 6.128 19914 Z= 0.258 Chirality : 0.036 0.184 2271 Planarity : 0.003 0.030 2073 Dihedral : 19.656 164.632 3292 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.89 % Allowed : 10.78 % Favored : 87.33 % 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: 0.83 (0.20), residues: 651 sheet: -0.90 (0.43), residues: 132 loop : -0.16 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 476 HIS 0.004 0.001 HIS P 116 PHE 0.014 0.001 PHE P1008 TYR 0.012 0.001 TYR P 155 ARG 0.005 0.000 ARG P 832 *********************** 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 92 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8555 (mt) cc_final: 0.8324 (mp) REVERT: P 433 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8199 (mp) REVERT: P 789 LYS cc_start: 0.9141 (ttpt) cc_final: 0.8856 (mmmt) REVERT: P 912 ASP cc_start: 0.7169 (m-30) cc_final: 0.6812 (m-30) REVERT: P 1037 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7932 (p90) outliers start: 23 outliers final: 15 residues processed: 89 average time/residue: 0.3544 time to fit residues: 46.0450 Evaluate side-chains 79 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 428 ASP Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 578 VAL Chi-restraints excluded: chain P residue 662 LEU Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 838 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 14346 Z= 0.474 Angle : 0.649 6.667 19914 Z= 0.338 Chirality : 0.043 0.194 2271 Planarity : 0.004 0.043 2073 Dihedral : 19.885 166.226 3292 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.39 % Allowed : 10.78 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1349 helix: 0.43 (0.20), residues: 649 sheet: -1.11 (0.43), residues: 132 loop : -0.29 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP P 476 HIS 0.005 0.001 HIS P 167 PHE 0.020 0.002 PHE P1008 TYR 0.018 0.002 TYR P 155 ARG 0.005 0.001 ARG P 78 *********************** 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 102 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 114 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: P 216 LEU cc_start: 0.8542 (mt) cc_final: 0.8280 (mp) REVERT: P 321 MET cc_start: 0.9319 (mmt) cc_final: 0.9056 (mmt) REVERT: P 433 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8333 (mp) REVERT: P 775 LYS cc_start: 0.8949 (mptt) cc_final: 0.8710 (mptt) REVERT: P 912 ASP cc_start: 0.7390 (m-30) cc_final: 0.7045 (m-30) outliers start: 29 outliers final: 15 residues processed: 98 average time/residue: 0.2725 time to fit residues: 40.2039 Evaluate side-chains 83 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain P residue 578 VAL Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 708 ILE Chi-restraints excluded: chain P residue 801 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1069 THR Chi-restraints excluded: chain P residue 1072 ILE Chi-restraints excluded: chain P residue 1179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14346 Z= 0.280 Angle : 0.538 6.080 19914 Z= 0.285 Chirality : 0.039 0.188 2271 Planarity : 0.003 0.029 2073 Dihedral : 19.856 172.408 3292 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.89 % Allowed : 11.69 % Favored : 86.42 % 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 (0.23), residues: 1349 helix: 0.55 (0.20), residues: 650 sheet: -1.08 (0.43), residues: 132 loop : -0.24 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 476 HIS 0.005 0.001 HIS P 116 PHE 0.018 0.001 PHE P1008 TYR 0.014 0.001 TYR P 155 ARG 0.002 0.000 ARG P1060 *********************** 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 91 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8551 (mt) cc_final: 0.8266 (mp) REVERT: P 321 MET cc_start: 0.9279 (mmt) cc_final: 0.9000 (mmt) REVERT: P 433 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8297 (mp) REVERT: P 912 ASP cc_start: 0.7338 (m-30) cc_final: 0.6999 (m-30) REVERT: P 1037 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7815 (p90) outliers start: 23 outliers final: 17 residues processed: 88 average time/residue: 0.2993 time to fit residues: 39.6685 Evaluate side-chains 85 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 95 ASP Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain P residue 476 TRP Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 578 VAL Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 708 ILE Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1006 SER Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE 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: 9.9990 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 0.0670 chunk 70 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14346 Z= 0.146 Angle : 0.471 6.958 19914 Z= 0.252 Chirality : 0.036 0.191 2271 Planarity : 0.003 0.029 2073 Dihedral : 19.645 175.704 3292 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.65 % Allowed : 12.18 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1349 helix: 0.81 (0.21), residues: 657 sheet: -0.79 (0.45), residues: 126 loop : -0.19 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 476 HIS 0.003 0.001 HIS P 328 PHE 0.013 0.001 PHE P1008 TYR 0.010 0.001 TYR P 814 ARG 0.002 0.000 ARG P 115 *********************** 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 100 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8461 (mt) cc_final: 0.8182 (mp) REVERT: P 775 LYS cc_start: 0.8941 (mptt) cc_final: 0.8686 (mptt) REVERT: P 781 MET cc_start: 0.8196 (mmm) cc_final: 0.7599 (mtp) REVERT: P 789 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8584 (mmmt) REVERT: P 1013 TYR cc_start: 0.7678 (m-80) cc_final: 0.7448 (m-10) REVERT: P 1037 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7864 (p90) outliers start: 20 outliers final: 11 residues processed: 97 average time/residue: 0.2948 time to fit residues: 42.3497 Evaluate side-chains 81 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 476 TRP Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 616 LEU Chi-restraints excluded: chain P residue 801 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8222 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14346 Z= 0.177 Angle : 0.477 7.142 19914 Z= 0.255 Chirality : 0.036 0.183 2271 Planarity : 0.003 0.028 2073 Dihedral : 19.592 172.900 3292 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.40 % Allowed : 12.59 % Favored : 86.01 % 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: 0.30 (0.23), residues: 1349 helix: 0.84 (0.20), residues: 657 sheet: -0.77 (0.44), residues: 126 loop : -0.18 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 476 HIS 0.004 0.001 HIS P 116 PHE 0.014 0.001 PHE P 916 TYR 0.013 0.001 TYR P 814 ARG 0.007 0.000 ARG P1084 *********************** 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 87 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8437 (mt) cc_final: 0.8179 (mp) REVERT: P 775 LYS cc_start: 0.8937 (mptt) cc_final: 0.8581 (mptt) REVERT: P 781 MET cc_start: 0.8222 (mmm) cc_final: 0.7643 (mtp) REVERT: P 789 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8603 (mmmt) REVERT: P 916 PHE cc_start: 0.8360 (m-10) cc_final: 0.8057 (m-10) REVERT: P 1013 TYR cc_start: 0.7677 (m-80) cc_final: 0.7462 (m-10) REVERT: P 1037 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7957 (p90) outliers start: 17 outliers final: 13 residues processed: 83 average time/residue: 0.2962 time to fit residues: 36.0741 Evaluate side-chains 81 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 428 ASP Chi-restraints excluded: chain P residue 476 TRP Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 578 VAL Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1006 SER Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1021 MET Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE 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: 0.8980 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 134 optimal weight: 0.0980 chunk 116 optimal weight: 0.0020 chunk 12 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 0.0970 chunk 92 optimal weight: 0.8980 overall best weight: 0.2384 ------------------------------------------------------------------------------- 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: 0.8170 moved from start: 0.3954 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= 0.121 Angle : 0.455 7.208 19914 Z= 0.245 Chirality : 0.035 0.179 2271 Planarity : 0.003 0.035 2073 Dihedral : 19.473 173.002 3292 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.32 % Allowed : 13.25 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1349 helix: 0.94 (0.21), residues: 657 sheet: -0.74 (0.45), residues: 128 loop : -0.15 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 476 HIS 0.003 0.001 HIS P 328 PHE 0.023 0.001 PHE P 972 TYR 0.010 0.001 TYR P 359 ARG 0.005 0.000 ARG P1084 ********************** 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 94 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8459 (mt) cc_final: 0.8215 (mp) REVERT: P 775 LYS cc_start: 0.8941 (mptt) cc_final: 0.8679 (mptt) REVERT: P 781 MET cc_start: 0.8237 (mmm) cc_final: 0.7619 (mtp) REVERT: P 789 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8536 (mmmt) REVERT: P 1037 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7963 (p90) outliers start: 16 outliers final: 15 residues processed: 91 average time/residue: 0.2856 time to fit residues: 38.8150 Evaluate side-chains 84 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 428 ASP Chi-restraints excluded: chain P residue 476 TRP Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 578 VAL Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1006 SER Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1021 MET Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE 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: 2.9990 chunk 107 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 826 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.102252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072862 restraints weight = 29266.219| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.22 r_work: 0.3027 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3996 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= 0.151 Angle : 0.457 6.907 19914 Z= 0.246 Chirality : 0.035 0.181 2271 Planarity : 0.003 0.030 2073 Dihedral : 19.420 170.274 3292 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.48 % Allowed : 13.50 % Favored : 85.02 % 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: 0.43 (0.23), residues: 1349 helix: 0.96 (0.21), residues: 661 sheet: -0.75 (0.45), residues: 128 loop : -0.13 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 476 HIS 0.003 0.001 HIS P 116 PHE 0.020 0.001 PHE P 916 TYR 0.011 0.001 TYR P 815 ARG 0.005 0.000 ARG P1084 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2634.04 seconds wall clock time: 49 minutes 17.53 seconds (2957.53 seconds total)