Starting phenix.real_space_refine on Thu Nov 16 02:17:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/11_2023/5vzl_8749_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/11_2023/5vzl_8749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/11_2023/5vzl_8749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/11_2023/5vzl_8749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/11_2023/5vzl_8749_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/11_2023/5vzl_8749_neut_updated.pdb" } resolution = 3.9 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= 0.000 sd= 0.005 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 118 5.49 5 S 25 5.16 5 C 8364 2.51 5 N 2420 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 919": "NH1" <-> "NH2" Residue "A ARG 1114": "NH1" <-> "NH2" Residue "A PHE 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1333": "NH1" <-> "NH2" Residue "A ARG 1335": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 13915 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2494 Unusual residues: {'GTP': 1} Classifications: {'RNA': 115, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 18, 'rna3p': 96, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "A" Number of atoms: 10711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10711 Classifications: {'peptide': 1364} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 35, 'TRANS': 1328} Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 220 Chain: "C" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.15, per 1000 atoms: 0.59 Number of scatterers: 13915 At special positions: 0 Unit cell: (112.35, 136.96, 120.91, 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 118 15.00 O 2988 8.00 N 2420 7.00 C 8364 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: 6.83 Conformation dependent library (CDL) restraints added in 2.5 seconds 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 9 sheets defined 43.5% alpha, 5.4% beta 30 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 10.03 Creating SS restraints... Processing helix chain 'A' and resid 60 through 85 Processing helix chain 'A' and resid 87 through 93 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.439A pdb=" N PHE A 98 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.866A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.865A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 271 through 281 removed outlier: 5.253A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 305 removed outlier: 3.625A pdb=" N ALA A 287 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP A 288 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 296 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 342 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 369 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.769A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 409' Processing helix chain 'A' and resid 412 through 425 removed outlier: 3.650A pdb=" N ILE A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 434 No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'A' and resid 437 through 444 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 513 through 526 removed outlier: 4.685A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 604 through 607 No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 613 through 625 Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.904A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 4.126A pdb=" N LEU A 651 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 693 through 697 Processing helix chain 'A' and resid 704 through 712 removed outlier: 3.860A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 731 through 750 Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 777 through 791 Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 809 through 816 Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'A' and resid 873 through 876 No H-bonds generated for 'chain 'A' and resid 873 through 876' Processing helix chain 'A' and resid 882 through 888 Processing helix chain 'A' and resid 894 through 905 removed outlier: 5.147A pdb=" N ALA A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A 905 " --> pdb=" O THR A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 removed outlier: 3.834A pdb=" N GLN A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 939 removed outlier: 3.592A pdb=" N ARG A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 980 through 1000 removed outlier: 3.831A pdb=" N HIS A 983 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 993 " --> pdb=" O ASN A 990 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 994 " --> pdb=" O ALA A 991 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 995 " --> pdb=" O VAL A 992 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A1000 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1007 No H-bonds generated for 'chain 'A' and resid 1005 through 1007' Processing helix chain 'A' and resid 1018 through 1021 No H-bonds generated for 'chain 'A' and resid 1018 through 1021' Processing helix chain 'A' and resid 1044 through 1046 No H-bonds generated for 'chain 'A' and resid 1044 through 1046' Processing helix chain 'A' and resid 1079 through 1087 Processing helix chain 'A' and resid 1128 through 1131 No H-bonds generated for 'chain 'A' and resid 1128 through 1131' Processing helix chain 'A' and resid 1168 through 1176 removed outlier: 5.943A pdb=" N SER A1172 " --> pdb=" O MET A1169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A1175 " --> pdb=" O SER A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1192 through 1194 No H-bonds generated for 'chain 'A' and resid 1192 through 1194' Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1230 through 1240 Processing helix chain 'A' and resid 1249 through 1261 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 3.663A pdb=" N ILE A1270 " --> pdb=" O ASP A1267 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A1273 " --> pdb=" O ILE A1270 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A1275 " --> pdb=" O GLN A1272 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A1276 " --> pdb=" O ILE A1273 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A1278 " --> pdb=" O GLU A1275 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A1280 " --> pdb=" O SER A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1296 Processing helix chain 'A' and resid 1302 through 1316 removed outlier: 4.344A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1344 No H-bonds generated for 'chain 'A' and resid 1342 through 1344' Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 51 through 58 Processing helix chain 'C' and resid 71 through 81 Processing sheet with id= A, first strand: chain 'A' and resid 6 through 11 removed outlier: 6.184A pdb=" N ASN A1093 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 52 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL A1095 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 29 through 33 Processing sheet with id= C, first strand: chain 'A' and resid 529 through 531 Processing sheet with id= D, first strand: chain 'A' and resid 758 through 761 removed outlier: 6.745A pdb=" N LYS A 954 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE A 761 " --> pdb=" O LYS A 954 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 956 " --> pdb=" O ILE A 761 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 837 through 840 Processing sheet with id= F, first strand: chain 'A' and resid 1196 through 1198 removed outlier: 4.037A pdb=" N VAL A1145 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A1162 " --> pdb=" O VAL A1145 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1203 through 1206 Processing sheet with id= H, first strand: chain 'A' and resid 1346 through 1349 Processing sheet with id= I, first strand: chain 'A' and resid 1063 through 1065 373 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 7.13 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: 2283 1.32 - 1.44: 4269 1.44 - 1.56: 7579 1.56 - 1.69: 234 1.69 - 1.81: 48 Bond restraints: 14413 Sorted by residual: bond pdb=" C3' A B 47 " pdb=" O3' A B 47 " ideal model delta sigma weight residual 1.427 1.453 -0.026 1.50e-02 4.44e+03 2.90e+00 bond pdb=" C GLY A1319 " pdb=" N ALA A1320 " ideal model delta sigma weight residual 1.340 1.243 0.098 5.87e-02 2.90e+02 2.77e+00 bond pdb=" N9 G B 4 " pdb=" C4 G B 4 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.03e+00 bond pdb=" CB PHE A 972 " pdb=" CG PHE A 972 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.97e+00 ... (remaining 14408 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.82: 770 105.82 - 113.54: 8409 113.54 - 121.26: 7241 121.26 - 128.98: 3473 128.98 - 136.70: 166 Bond angle restraints: 20059 Sorted by residual: angle pdb=" N VAL A1015 " pdb=" CA VAL A1015 " pdb=" C VAL A1015 " ideal model delta sigma weight residual 111.91 106.73 5.18 8.90e-01 1.26e+00 3.38e+01 angle pdb=" C3' A B 47 " pdb=" O3' A B 47 " pdb=" P A B 48 " ideal model delta sigma weight residual 120.20 127.23 -7.03 1.50e+00 4.44e-01 2.20e+01 angle pdb=" CA ARG C 33 " pdb=" CB ARG C 33 " pdb=" CG ARG C 33 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" C PHE A 196 " pdb=" N GLU A 197 " pdb=" CA GLU A 197 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C3' A B 86 " pdb=" O3' A B 86 " pdb=" P A B 87 " ideal model delta sigma weight residual 120.20 126.54 -6.34 1.50e+00 4.44e-01 1.79e+01 ... (remaining 20054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 8268 35.20 - 70.39: 157 70.39 - 105.59: 18 105.59 - 140.78: 4 140.78 - 175.98: 5 Dihedral angle restraints: 8452 sinusoidal: 4186 harmonic: 4266 Sorted by residual: dihedral pdb=" O4' C B 88 " pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sinusoidal sigma weight residual 200.00 39.82 160.18 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U B 7 " pdb=" C1' U B 7 " pdb=" N1 U B 7 " pdb=" C2 U B 7 " ideal model delta sinusoidal sigma weight residual 232.00 56.02 175.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N GLU C 47 " pdb=" CA GLU C 47 " ideal model delta harmonic sigma weight residual 180.00 143.46 36.54 0 5.00e+00 4.00e-02 5.34e+01 ... (remaining 8449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1930 0.062 - 0.125: 377 0.125 - 0.187: 39 0.187 - 0.250: 8 0.250 - 0.312: 2 Chirality restraints: 2356 Sorted by residual: chirality pdb=" C3' C B 35 " pdb=" C4' C B 35 " pdb=" O3' C B 35 " pdb=" C2' C B 35 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C3' A B 47 " pdb=" C4' A B 47 " pdb=" O3' A B 47 " pdb=" C2' A B 47 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" P A B 48 " pdb=" OP1 A B 48 " pdb=" OP2 A B 48 " pdb=" O5' A B 48 " both_signs ideal model delta sigma weight residual True 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2353 not shown) Planarity restraints: 2153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 47 " 0.040 2.00e-02 2.50e+03 1.79e-02 8.80e+00 pdb=" N9 A B 47 " -0.038 2.00e-02 2.50e+03 pdb=" C8 A B 47 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A B 47 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A B 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 47 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 47 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A B 47 " 0.013 2.00e-02 2.50e+03 pdb=" C2 A B 47 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A B 47 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A B 47 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 271 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C TYR A 271 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR A 271 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 272 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1326 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C TYR A1326 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR A1326 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A1327 " 0.016 2.00e-02 2.50e+03 ... (remaining 2150 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2084 2.75 - 3.29: 13482 3.29 - 3.83: 24619 3.83 - 4.36: 28142 4.36 - 4.90: 42832 Nonbonded interactions: 111159 Sorted by model distance: nonbonded pdb=" O2' G B 61 " pdb=" OH TYR A 359 " model vdw 2.216 2.440 nonbonded pdb=" O GLN C 78 " pdb=" OG1 THR C 81 " model vdw 2.239 2.440 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR A 474 " pdb=" OD1 ASN A 477 " model vdw 2.273 2.440 nonbonded pdb=" OG1 THR A 560 " pdb=" OD1 ASP A 585 " model vdw 2.296 2.440 ... (remaining 111154 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 46.400 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0248 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 : 0.006 0.098 14413 Z= 0.368 Angle : 0.958 12.390 20059 Z= 0.508 Chirality : 0.050 0.312 2356 Planarity : 0.006 0.068 2153 Dihedral : 14.276 175.978 5692 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.25 % Allowed : 3.33 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -4.13 (0.17), residues: 1447 helix: -2.93 (0.14), residues: 661 sheet: -1.64 (0.49), residues: 110 loop : -2.64 (0.21), residues: 676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 124 average time/residue: 0.3312 time to fit residues: 57.5707 Evaluate side-chains 80 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.0050 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 chunk 73 optimal weight: 0.0050 chunk 90 optimal weight: 0.0270 chunk 140 optimal weight: 0.0030 overall best weight: 0.0676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 137 HIS A 194 GLN A 224 ASN A 522 ASN A 595 HIS A 609 ASN A 709 GLN A 767 ASN A 899 ASN A1286 ASN C 2 ASN C 12 ASN C 25 ASN C 36 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0343 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14413 Z= 0.133 Angle : 0.558 8.810 20059 Z= 0.288 Chirality : 0.037 0.240 2356 Planarity : 0.004 0.056 2153 Dihedral : 15.259 177.444 2966 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.00 % Allowed : 6.67 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.62 (0.20), residues: 1447 helix: -1.18 (0.18), residues: 684 sheet: -1.58 (0.46), residues: 118 loop : -2.34 (0.22), residues: 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.411 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 0.2766 time to fit residues: 40.5910 Evaluate side-chains 85 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1231 time to fit residues: 3.2489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 HIS A1308 ASN A1317 ASN C 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0686 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14413 Z= 0.169 Angle : 0.571 8.719 20059 Z= 0.296 Chirality : 0.038 0.233 2356 Planarity : 0.004 0.073 2153 Dihedral : 14.748 179.796 2966 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.58 % Allowed : 7.50 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.90 (0.20), residues: 1447 helix: -0.53 (0.19), residues: 682 sheet: -0.94 (0.48), residues: 103 loop : -2.09 (0.22), residues: 662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 106 average time/residue: 0.2864 time to fit residues: 45.1831 Evaluate side-chains 85 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1463 time to fit residues: 4.1553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 415 HIS ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN A 817 GLN A 899 ASN A 920 GLN A1295 ASN C 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1482 moved from start: 0.7490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 14413 Z= 0.370 Angle : 0.984 12.042 20059 Z= 0.509 Chirality : 0.052 0.296 2356 Planarity : 0.007 0.067 2153 Dihedral : 16.006 172.693 2966 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.78 % Favored : 91.15 % Rotamer: Outliers : 2.75 % Allowed : 10.25 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.89 (0.19), residues: 1447 helix: -1.47 (0.18), residues: 650 sheet: -1.16 (0.47), residues: 98 loop : -2.47 (0.21), residues: 699 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 10 residues processed: 128 average time/residue: 0.2892 time to fit residues: 54.0451 Evaluate side-chains 96 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1411 time to fit residues: 4.4574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 61 optimal weight: 0.0020 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN A 309 ASN A 723 HIS A 982 HIS A1286 ASN A1295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1261 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14413 Z= 0.155 Angle : 0.617 12.577 20059 Z= 0.313 Chirality : 0.040 0.215 2356 Planarity : 0.004 0.057 2153 Dihedral : 14.962 174.241 2966 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.75 % Allowed : 12.33 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.21 (0.20), residues: 1447 helix: -0.89 (0.19), residues: 652 sheet: -0.45 (0.53), residues: 88 loop : -2.17 (0.21), residues: 707 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 0.3109 time to fit residues: 41.4453 Evaluate side-chains 79 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1645 time to fit residues: 2.7856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 240 ASN A 723 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1333 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14413 Z= 0.162 Angle : 0.602 10.097 20059 Z= 0.305 Chirality : 0.039 0.220 2356 Planarity : 0.004 0.067 2153 Dihedral : 14.666 173.297 2966 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.25 % Allowed : 14.17 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.96 (0.20), residues: 1447 helix: -0.66 (0.19), residues: 649 sheet: -0.54 (0.51), residues: 100 loop : -2.04 (0.21), residues: 698 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 104 average time/residue: 0.2893 time to fit residues: 44.7238 Evaluate side-chains 84 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1253 time to fit residues: 2.9160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.0970 chunk 85 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 93 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 723 HIS A1234 ASN A1241 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1380 moved from start: 0.8820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14413 Z= 0.166 Angle : 0.599 12.611 20059 Z= 0.303 Chirality : 0.039 0.232 2356 Planarity : 0.004 0.046 2153 Dihedral : 14.600 173.250 2966 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.17 % Allowed : 14.83 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.89 (0.21), residues: 1447 helix: -0.59 (0.20), residues: 651 sheet: -0.62 (0.50), residues: 100 loop : -2.01 (0.22), residues: 696 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 1.255 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.2695 time to fit residues: 36.0357 Evaluate side-chains 83 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1311 time to fit residues: 3.4516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1679 moved from start: 1.0379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14413 Z= 0.263 Angle : 0.791 11.026 20059 Z= 0.403 Chirality : 0.045 0.241 2356 Planarity : 0.006 0.070 2153 Dihedral : 15.443 170.162 2966 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 1.75 % Allowed : 14.17 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.47 (0.20), residues: 1447 helix: -1.10 (0.19), residues: 644 sheet: -1.18 (0.47), residues: 105 loop : -2.24 (0.21), residues: 698 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 103 average time/residue: 0.2433 time to fit residues: 37.5140 Evaluate side-chains 93 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1469 time to fit residues: 4.7770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN A 354 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN C 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1665 moved from start: 1.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14413 Z= 0.206 Angle : 0.687 13.064 20059 Z= 0.348 Chirality : 0.042 0.235 2356 Planarity : 0.005 0.066 2153 Dihedral : 15.319 173.827 2966 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.25 % Allowed : 14.67 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.40 (0.20), residues: 1447 helix: -0.99 (0.19), residues: 650 sheet: -0.97 (0.51), residues: 98 loop : -2.27 (0.21), residues: 699 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 94 average time/residue: 0.2789 time to fit residues: 39.9009 Evaluate side-chains 83 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 154 optimal weight: 0.4980 chunk 142 optimal weight: 0.0000 chunk 122 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN A 899 ASN ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1567 moved from start: 1.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14413 Z= 0.143 Angle : 0.612 11.308 20059 Z= 0.305 Chirality : 0.039 0.224 2356 Planarity : 0.004 0.049 2153 Dihedral : 14.978 175.910 2966 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.58 % Allowed : 15.08 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.05 (0.21), residues: 1447 helix: -0.65 (0.20), residues: 652 sheet: -0.89 (0.51), residues: 98 loop : -2.14 (0.22), residues: 697 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.375 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 89 average time/residue: 0.2690 time to fit residues: 36.9174 Evaluate side-chains 80 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1452 time to fit residues: 2.5123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.0030 chunk 37 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 309 ASN ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.256609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.226489 restraints weight = 32412.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.228692 restraints weight = 20830.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.230740 restraints weight = 13276.292| |-----------------------------------------------------------------------------| r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2154 moved from start: 1.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14413 Z= 0.225 Angle : 0.738 11.179 20059 Z= 0.372 Chirality : 0.043 0.233 2356 Planarity : 0.005 0.061 2153 Dihedral : 15.419 173.842 2966 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.58 % Allowed : 16.08 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.28 (0.20), residues: 1447 helix: -0.87 (0.19), residues: 651 sheet: -1.11 (0.49), residues: 105 loop : -2.20 (0.22), residues: 691 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2402.89 seconds wall clock time: 50 minutes 2.32 seconds (3002.32 seconds total)