Starting phenix.real_space_refine on Sun Dec 10 08:35:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/12_2023/5vzl_8749_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/12_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_8749/12_2023/5vzl_8749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/12_2023/5vzl_8749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/12_2023/5vzl_8749_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/12_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-1.21rc1-5172/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: 7.77, per 1000 atoms: 0.56 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: 6.35 Conformation dependent library (CDL) restraints added in 2.1 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: 7.21 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: 6.04 Time building geometry restraints manager: 6.77 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: 8380 35.20 - 70.39: 270 70.39 - 105.59: 37 105.59 - 140.78: 4 140.78 - 175.98: 5 Dihedral angle restraints: 8696 sinusoidal: 4430 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 8693 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.230 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 44.850 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.680 ------------------------------------------------------------------------------- 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 : 16.646 175.978 5936 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 464 HIS 0.007 0.002 HIS A1241 PHE 0.020 0.003 PHE A1008 TYR 0.028 0.003 TYR A 973 ARG 0.015 0.001 ARG A 78 *********************** 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 : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 124 average time/residue: 0.3494 time to fit residues: 60.7058 Evaluate side-chains 80 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9331 ------------------------------------------------------------------------------- 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: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 14413 Z= 0.144 Angle : 0.559 8.800 20059 Z= 0.288 Chirality : 0.037 0.243 2356 Planarity : 0.004 0.056 2153 Dihedral : 19.064 177.609 3210 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.00 % Allowed : 6.42 % Favored : 92.58 % 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: -1.16 (0.18), residues: 684 sheet: -1.70 (0.45), residues: 121 loop : -2.35 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.004 0.001 HIS A 328 PHE 0.017 0.001 PHE A 32 TYR 0.017 0.001 TYR A 155 ARG 0.004 0.000 ARG A 976 *********************** 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 99 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 98 average time/residue: 0.2196 time to fit residues: 32.1375 Evaluate side-chains 85 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1033 time to fit residues: 2.6292 ------------------------------------------------------------------------------- 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: 6.9990 chunk 43 optimal weight: 0.6980 chunk 117 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 501 ASN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN A1091 GLN A1317 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0606 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14413 Z= 0.155 Angle : 0.536 8.568 20059 Z= 0.277 Chirality : 0.037 0.229 2356 Planarity : 0.004 0.069 2153 Dihedral : 18.646 179.927 3210 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.42 % Allowed : 7.50 % Favored : 91.08 % 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: -1.82 (0.21), residues: 1447 helix: -0.43 (0.19), residues: 687 sheet: -0.94 (0.49), residues: 103 loop : -2.10 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 PHE 0.014 0.002 PHE C 73 TYR 0.015 0.001 TYR A 136 ARG 0.010 0.001 ARG A 976 *********************** 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 109 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.307 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 104 average time/residue: 0.2804 time to fit residues: 43.1597 Evaluate side-chains 81 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1395 time to fit residues: 3.3722 ------------------------------------------------------------------------------- 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: 1.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 141 optimal weight: 0.7980 chunk 149 optimal weight: 0.0370 chunk 134 optimal weight: 0.6980 chunk 40 optimal weight: 0.0050 chunk 124 optimal weight: 4.9990 overall best weight: 0.5074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 ASN A 817 GLN A 863 ASN A 899 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0682 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14413 Z= 0.127 Angle : 0.498 8.714 20059 Z= 0.257 Chirality : 0.036 0.209 2356 Planarity : 0.003 0.039 2153 Dihedral : 18.413 179.117 3210 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.08 % Allowed : 9.67 % Favored : 89.25 % 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: -1.42 (0.21), residues: 1447 helix: -0.00 (0.20), residues: 680 sheet: -0.99 (0.47), residues: 112 loop : -1.94 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS A 116 PHE 0.014 0.001 PHE A 704 TYR 0.013 0.001 TYR A 836 ARG 0.006 0.000 ARG A 976 *********************** 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 91 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 89 average time/residue: 0.2783 time to fit residues: 37.1917 Evaluate side-chains 76 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2228 time to fit residues: 3.4872 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN A 920 GLN A1091 GLN A1264 HIS A1295 ASN C 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1494 moved from start: 0.7721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 14413 Z= 0.373 Angle : 0.985 11.356 20059 Z= 0.505 Chirality : 0.052 0.310 2356 Planarity : 0.007 0.062 2153 Dihedral : 19.412 171.367 3210 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.57 % Favored : 91.29 % Rotamer: Outliers : 2.42 % Allowed : 10.00 % Favored : 87.58 % 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: -2.66 (0.20), residues: 1447 helix: -1.31 (0.18), residues: 649 sheet: -1.01 (0.56), residues: 78 loop : -2.29 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 476 HIS 0.016 0.003 HIS A 167 PHE 0.035 0.004 PHE A1181 TYR 0.032 0.004 TYR A 515 ARG 0.014 0.002 ARG A 221 *********************** 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 131 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 121 average time/residue: 0.2874 time to fit residues: 51.8106 Evaluate side-chains 98 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1451 time to fit residues: 5.2573 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 124 optimal weight: 0.0060 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 415 HIS A 723 HIS ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1286 moved from start: 0.7764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14413 Z= 0.154 Angle : 0.609 14.788 20059 Z= 0.311 Chirality : 0.040 0.219 2356 Planarity : 0.004 0.047 2153 Dihedral : 18.672 173.275 3210 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.67 % Allowed : 12.33 % Favored : 87.00 % 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: -2.02 (0.21), residues: 1447 helix: -0.75 (0.19), residues: 653 sheet: -0.50 (0.51), residues: 98 loop : -2.04 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 PHE 0.027 0.002 PHE A 491 TYR 0.028 0.002 TYR A1237 ARG 0.005 0.001 ARG A 400 *********************** 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 90 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 0.2805 time to fit residues: 37.6992 Evaluate side-chains 77 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1884 time to fit residues: 2.5753 ------------------------------------------------------------------------------- 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: 5.9990 chunk 85 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 91 optimal weight: 0.4980 chunk 68 optimal weight: 0.0470 chunk 92 optimal weight: 6.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 240 ASN A 341 GLN A 412 HIS A 723 HIS ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1264 moved from start: 0.8106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14413 Z= 0.138 Angle : 0.553 12.573 20059 Z= 0.280 Chirality : 0.038 0.224 2356 Planarity : 0.004 0.047 2153 Dihedral : 18.347 174.470 3210 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.00 % Allowed : 13.25 % Favored : 85.75 % 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: -1.66 (0.21), residues: 1447 helix: -0.37 (0.20), residues: 650 sheet: -0.35 (0.52), residues: 99 loop : -1.93 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 PHE 0.020 0.002 PHE A 704 TYR 0.015 0.001 TYR A 373 ARG 0.007 0.000 ARG A 655 *********************** 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 102 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 99 average time/residue: 0.2824 time to fit residues: 41.3500 Evaluate side-chains 86 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1404 time to fit residues: 3.1899 ------------------------------------------------------------------------------- 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: 0.0570 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 73 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 117 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 HIS A 758 ASN A1241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1245 moved from start: 0.8425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14413 Z= 0.123 Angle : 0.531 10.386 20059 Z= 0.267 Chirality : 0.037 0.213 2356 Planarity : 0.003 0.046 2153 Dihedral : 18.202 174.744 3210 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.33 % Allowed : 13.92 % Favored : 85.75 % 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: -1.41 (0.21), residues: 1447 helix: -0.14 (0.20), residues: 651 sheet: -0.23 (0.54), residues: 96 loop : -1.83 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 476 HIS 0.009 0.001 HIS A1241 PHE 0.020 0.001 PHE A 119 TYR 0.019 0.001 TYR A 656 ARG 0.003 0.000 ARG A 340 *********************** 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 85 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 84 average time/residue: 0.2973 time to fit residues: 36.9675 Evaluate side-chains 75 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9193 ------------------------------------------------------------------------------- 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: 0.9980 chunk 130 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** A 899 ASN A 985 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1350 moved from start: 0.8928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14413 Z= 0.143 Angle : 0.560 10.948 20059 Z= 0.280 Chirality : 0.038 0.215 2356 Planarity : 0.004 0.068 2153 Dihedral : 18.244 173.542 3210 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.75 % Allowed : 13.75 % Favored : 85.50 % 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: -1.41 (0.21), residues: 1447 helix: -0.16 (0.20), residues: 648 sheet: -0.58 (0.49), residues: 108 loop : -1.75 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 PHE 0.023 0.002 PHE A 119 TYR 0.023 0.002 TYR A 656 ARG 0.006 0.000 ARG A1122 *********************** 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: 9 poor density : 86 time to evaluate : 1.203 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 93 average time/residue: 0.2805 time to fit residues: 38.7201 Evaluate side-chains 87 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2289 time to fit residues: 3.9138 ------------------------------------------------------------------------------- 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: 0.0870 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.0070 chunk 102 optimal weight: 0.6980 chunk 154 optimal weight: 0.0070 chunk 142 optimal weight: 0.2980 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 75 optimal weight: 0.0670 chunk 97 optimal weight: 10.0000 overall best weight: 0.0932 ------------------------------------------------------------------------------- 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** A 985 HIS A1295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1197 moved from start: 0.8903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14413 Z= 0.109 Angle : 0.512 12.055 20059 Z= 0.255 Chirality : 0.036 0.204 2356 Planarity : 0.003 0.054 2153 Dihedral : 17.996 176.033 3210 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.17 % Allowed : 13.67 % Favored : 86.17 % 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: -1.19 (0.22), residues: 1447 helix: 0.16 (0.21), residues: 656 sheet: -0.32 (0.50), residues: 106 loop : -1.83 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.009 0.001 HIS A1241 PHE 0.024 0.001 PHE A 119 TYR 0.020 0.001 TYR A 325 ARG 0.003 0.000 ARG A 70 ********************** 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 77 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 77 average time/residue: 0.2822 time to fit residues: 32.7535 Evaluate side-chains 73 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1593 time to fit residues: 2.2310 ------------------------------------------------------------------------------- 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: 0.4980 chunk 37 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN A 985 HIS A1295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.260541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.231204 restraints weight = 32149.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.235276 restraints weight = 18447.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.236772 restraints weight = 10477.836| |-----------------------------------------------------------------------------| r_work (final): 0.4814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1824 moved from start: 0.9944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14413 Z= 0.195 Angle : 0.643 9.840 20059 Z= 0.325 Chirality : 0.040 0.205 2356 Planarity : 0.004 0.051 2153 Dihedral : 18.407 171.545 3210 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.42 % Allowed : 13.58 % Favored : 86.00 % 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: -1.58 (0.21), residues: 1447 helix: -0.31 (0.20), residues: 649 sheet: -0.86 (0.48), residues: 113 loop : -1.79 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 476 HIS 0.010 0.002 HIS A1264 PHE 0.025 0.002 PHE A 119 TYR 0.028 0.002 TYR A 656 ARG 0.006 0.001 ARG A 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2343.49 seconds wall clock time: 46 minutes 19.41 seconds (2779.41 seconds total)