Starting phenix.real_space_refine on Mon Apr 8 23:50:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhc_18407/04_2024/8qhc_18407_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhc_18407/04_2024/8qhc_18407.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhc_18407/04_2024/8qhc_18407_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhc_18407/04_2024/8qhc_18407_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhc_18407/04_2024/8qhc_18407_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhc_18407/04_2024/8qhc_18407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhc_18407/04_2024/8qhc_18407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhc_18407/04_2024/8qhc_18407_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhc_18407/04_2024/8qhc_18407_updated.pdb" } resolution = 3.1 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= 0.006 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: 6 Type Number sf(0) Gaussians P 64 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 9190 2.51 5 N 2523 2.21 5 O 3011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 167": "OD1" <-> "OD2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1343": "OD1" <-> "OD2" Residue "A PHE 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1410": "OD1" <-> "OD2" Residue "A TYR 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 182": "OD1" <-> "OD2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14829 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2937 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 372} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1309 Classifications: {'RNA': 61} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p': 6, 'rna3p_pur': 21, 'rna3p_pyr': 20} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 9015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9015 Classifications: {'peptide': 1183} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 42, 'TRANS': 1140} Chain breaks: 14 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 588 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 32, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 301 Chain: "D" Number of atoms: 1535 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 12, 'TRANS': 175} Conformer: "B" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 12, 'TRANS': 175} bond proxies already assigned to first conformer: 1549 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.10, per 1000 atoms: 0.61 Number of scatterers: 14829 At special positions: 0 Unit cell: (138.936, 122.396, 153.822, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 64 15.00 Mg 1 11.99 O 3011 8.00 N 2523 7.00 C 9190 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=0, symmetry=0 Time building additional restraints: 6.57 Conformation dependent library (CDL) restraints added in 2.7 seconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3350 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 6 sheets defined 59.9% alpha, 5.8% beta 21 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 7.18 Creating SS restraints... Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.700A pdb=" N VAL C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 126 Processing helix chain 'C' and resid 145 through 161 removed outlier: 3.597A pdb=" N TYR C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 183 through 198 removed outlier: 3.578A pdb=" N LYS C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 18 through 33 Processing helix chain 'A' and resid 41 through 47 removed outlier: 3.803A pdb=" N TYR A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 87 Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 127 through 139 Proline residue: A 135 - end of helix removed outlier: 4.478A pdb=" N LYS A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.601A pdb=" N ASN A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 204 removed outlier: 4.288A pdb=" N LEU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 318 through 338 Processing helix chain 'A' and resid 389 through 410 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 445 through 465 removed outlier: 4.218A pdb=" N GLN A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 467 through 478 removed outlier: 3.774A pdb=" N LYS A 471 " --> pdb=" O PRO A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 488 No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 502 through 546 removed outlier: 3.793A pdb=" N CYS A 509 " --> pdb=" O GLN A 505 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N SER A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 606 Processing helix chain 'A' and resid 622 through 638 removed outlier: 3.919A pdb=" N THR A 631 " --> pdb=" O LYS A 627 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Proline residue: A 634 - end of helix Processing helix chain 'A' and resid 642 through 653 removed outlier: 3.723A pdb=" N SER A 650 " --> pdb=" O THR A 646 " (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 669 through 706 removed outlier: 4.099A pdb=" N SER A 672 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLY A 673 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 719 removed outlier: 4.004A pdb=" N GLN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 728 removed outlier: 3.737A pdb=" N LEU A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 740 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 752 through 758 removed outlier: 4.021A pdb=" N GLN A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 758 " --> pdb=" O VAL A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 780 through 804 Processing helix chain 'A' and resid 822 through 843 Processing helix chain 'A' and resid 849 through 862 Proline residue: A 861 - end of helix Processing helix chain 'A' and resid 885 through 896 Processing helix chain 'A' and resid 910 through 925 Processing helix chain 'A' and resid 935 through 954 removed outlier: 4.306A pdb=" N GLY A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 978 Processing helix chain 'A' and resid 984 through 1013 Processing helix chain 'A' and resid 1020 through 1038 Processing helix chain 'A' and resid 1242 through 1258 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1277 through 1288 Processing helix chain 'A' and resid 1297 through 1311 Processing helix chain 'A' and resid 1328 through 1348 Processing helix chain 'A' and resid 1355 through 1368 Processing helix chain 'A' and resid 1389 through 1408 Processing helix chain 'A' and resid 1412 through 1420 Processing helix chain 'A' and resid 1425 through 1439 Proline residue: A1434 - end of helix Processing helix chain 'A' and resid 1501 through 1510 removed outlier: 3.751A pdb=" N PHE A1505 " --> pdb=" O ILE A1501 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N HIS A1509 " --> pdb=" O PHE A1505 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS A1510 " --> pdb=" O GLU A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1527 Processing helix chain 'A' and resid 1533 through 1553 Proline residue: A1548 - end of helix removed outlier: 4.470A pdb=" N LYS A1552 " --> pdb=" O PRO A1548 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A1553 " --> pdb=" O HIS A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1564 No H-bonds generated for 'chain 'A' and resid 1561 through 1564' Processing helix chain 'A' and resid 1569 through 1617 removed outlier: 3.919A pdb=" N ASP A1582 " --> pdb=" O ARG A1578 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A1583 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER A1584 " --> pdb=" O ILE A1580 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LYS A1585 " --> pdb=" O ASN A1581 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 31 removed outlier: 3.577A pdb=" N LEU D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 73 removed outlier: 4.088A pdb=" N LYS D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 3.786A pdb=" N ILE D 97 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE D 98 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN D 100 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASN D 114 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN D 119 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.775A pdb=" N PHE D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 188 through 203 Processing sheet with id= A, first strand: chain 'C' and resid 170 through 172 removed outlier: 9.124A pdb=" N VAL C 171 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL C 133 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 102 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N PHE C 134 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 104 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN C 136 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 106 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 212 through 214 Processing sheet with id= C, first strand: chain 'C' and resid 217 through 221 removed outlier: 3.575A pdb=" N ASP C 217 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR C 226 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 336 through 339 removed outlier: 6.357A pdb=" N GLU C 379 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 304 through 306 removed outlier: 6.286A pdb=" N GLU C 306 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL C 392 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 148 through 150 774 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 6.17 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2354 1.29 - 1.42: 3877 1.42 - 1.55: 8791 1.55 - 1.68: 130 1.68 - 1.81: 68 Bond restraints: 15220 Sorted by residual: bond pdb=" C4 5MU B 54 " pdb=" C5 5MU B 54 " ideal model delta sigma weight residual 1.802 1.445 0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" N1 5MU B 54 " pdb=" C6 5MU B 54 " ideal model delta sigma weight residual 1.635 1.369 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" N3 5MU B 54 " pdb=" C4 5MU B 54 " ideal model delta sigma weight residual 1.182 1.378 -0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C5 5MU B 54 " pdb=" C6 5MU B 54 " ideal model delta sigma weight residual 1.155 1.338 -0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" N1 H2U B 16 " pdb=" C2 H2U B 16 " ideal model delta sigma weight residual 1.482 1.350 0.132 2.00e-02 2.50e+03 4.34e+01 ... (remaining 15215 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.37: 508 105.37 - 112.53: 8137 112.53 - 119.68: 5019 119.68 - 126.84: 6996 126.84 - 134.00: 263 Bond angle restraints: 20923 Sorted by residual: angle pdb=" C6 5MU B 54 " pdb=" C5 5MU B 54 " pdb=" C5M 5MU B 54 " ideal model delta sigma weight residual 106.09 123.11 -17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" CA PRO D 91 " pdb=" N PRO D 91 " pdb=" CD PRO D 91 " ideal model delta sigma weight residual 112.00 105.78 6.22 1.40e+00 5.10e-01 1.97e+01 angle pdb=" N3 5MU B 54 " pdb=" C4 5MU B 54 " pdb=" O4 5MU B 54 " ideal model delta sigma weight residual 107.56 120.42 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" N LEU A 862 " pdb=" CA LEU A 862 " pdb=" C LEU A 862 " ideal model delta sigma weight residual 114.56 109.20 5.36 1.27e+00 6.20e-01 1.78e+01 angle pdb=" O4 5MU B 54 " pdb=" C4 5MU B 54 " pdb=" C5 5MU B 54 " ideal model delta sigma weight residual 112.86 125.09 -12.23 3.00e+00 1.11e-01 1.66e+01 ... (remaining 20918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 8871 35.45 - 70.91: 400 70.91 - 106.36: 45 106.36 - 141.81: 2 141.81 - 177.26: 6 Dihedral angle restraints: 9324 sinusoidal: 4163 harmonic: 5161 Sorted by residual: dihedral pdb=" O4' C B 75 " pdb=" C1' C B 75 " pdb=" N1 C B 75 " pdb=" C2 C B 75 " ideal model delta sinusoidal sigma weight residual 232.00 55.68 176.32 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B 17 " pdb=" C1' C B 17 " pdb=" N1 C B 17 " pdb=" C2 C B 17 " ideal model delta sinusoidal sigma weight residual -128.00 45.01 -173.01 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" C8 GTP C 402 " pdb=" C1* GTP C 402 " pdb=" N9 GTP C 402 " pdb=" O4* GTP C 402 " ideal model delta sinusoidal sigma weight residual 104.59 -59.90 164.50 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2189 0.063 - 0.125: 253 0.125 - 0.188: 12 0.188 - 0.250: 3 0.250 - 0.313: 1 Chirality restraints: 2458 Sorted by residual: chirality pdb=" CG LEU A1586 " pdb=" CB LEU A1586 " pdb=" CD1 LEU A1586 " pdb=" CD2 LEU A1586 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB ILE A1612 " pdb=" CA ILE A1612 " pdb=" CG1 ILE A1612 " pdb=" CG2 ILE A1612 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C3' G B 70 " pdb=" C4' G B 70 " pdb=" O3' G B 70 " pdb=" C2' G B 70 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2455 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' H2U B 16 " -0.001 2.00e-02 2.50e+03 5.50e-01 6.80e+03 pdb=" C4' H2U B 16 " -0.424 2.00e-02 2.50e+03 pdb=" O4' H2U B 16 " -0.648 2.00e-02 2.50e+03 pdb=" C3' H2U B 16 " 0.589 2.00e-02 2.50e+03 pdb=" O3' H2U B 16 " 0.502 2.00e-02 2.50e+03 pdb=" C2' H2U B 16 " 0.239 2.00e-02 2.50e+03 pdb=" O2' H2U B 16 " -0.850 2.00e-02 2.50e+03 pdb=" C1' H2U B 16 " -0.235 2.00e-02 2.50e+03 pdb=" N1 H2U B 16 " 0.828 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU B 54 " 0.025 2.00e-02 2.50e+03 5.50e-01 6.80e+03 pdb=" C4' 5MU B 54 " 0.427 2.00e-02 2.50e+03 pdb=" O4' 5MU B 54 " 0.589 2.00e-02 2.50e+03 pdb=" C3' 5MU B 54 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 5MU B 54 " -0.539 2.00e-02 2.50e+03 pdb=" C2' 5MU B 54 " -0.220 2.00e-02 2.50e+03 pdb=" O2' 5MU B 54 " 0.887 2.00e-02 2.50e+03 pdb=" C1' 5MU B 54 " 0.233 2.00e-02 2.50e+03 pdb=" N1 5MU B 54 " -0.817 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' H2U B 20 " -0.038 2.00e-02 2.50e+03 5.44e-01 6.65e+03 pdb=" C4' H2U B 20 " -0.417 2.00e-02 2.50e+03 pdb=" O4' H2U B 20 " -0.550 2.00e-02 2.50e+03 pdb=" C3' H2U B 20 " 0.585 2.00e-02 2.50e+03 pdb=" O3' H2U B 20 " 0.542 2.00e-02 2.50e+03 pdb=" C2' H2U B 20 " 0.212 2.00e-02 2.50e+03 pdb=" O2' H2U B 20 " -0.899 2.00e-02 2.50e+03 pdb=" C1' H2U B 20 " -0.235 2.00e-02 2.50e+03 pdb=" N1 H2U B 20 " 0.799 2.00e-02 2.50e+03 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 125 2.52 - 3.12: 11215 3.12 - 3.71: 25135 3.71 - 4.31: 33895 4.31 - 4.90: 55040 Nonbonded interactions: 125410 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb=" O2B GTP C 402 " model vdw 1.929 2.170 nonbonded pdb=" OG1 THR C 62 " pdb="MG MG C 401 " model vdw 2.038 2.170 nonbonded pdb=" OG1 THR C 26 " pdb="MG MG C 401 " model vdw 2.128 2.170 nonbonded pdb=" OG1 THR C 339 " pdb=" O2' G B 65 " model vdw 2.158 2.440 nonbonded pdb=" O LEU A 30 " pdb=" OG1 THR A 34 " model vdw 2.170 2.440 ... (remaining 125405 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=0.16 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 13.290 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 48.080 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 0.357 15220 Z= 0.316 Angle : 0.654 17.022 20923 Z= 0.316 Chirality : 0.040 0.313 2458 Planarity : 0.020 0.550 2456 Dihedral : 19.586 177.263 5974 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 22.60 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1731 helix: 2.00 (0.16), residues: 1063 sheet: -0.58 (0.47), residues: 122 loop : -0.80 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 70 HIS 0.008 0.001 HIS C 119 PHE 0.015 0.001 PHE A 600 TYR 0.020 0.001 TYR A 198 ARG 0.006 0.000 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.659 Fit side-chains revert: symmetry clash REVERT: A 1611 PHE cc_start: 0.7778 (m-80) cc_final: 0.7421 (m-80) REVERT: A 1618 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7377 (pp30) REVERT: D 102 PHE cc_start: 0.8955 (t80) cc_final: 0.8643 (t80) REVERT: D 159 GLN cc_start: 0.8936 (tt0) cc_final: 0.8423 (tm-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3006 time to fit residues: 52.4351 Evaluate side-chains 106 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 0.7980 chunk 137 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15220 Z= 0.221 Angle : 0.706 14.523 20923 Z= 0.384 Chirality : 0.040 0.231 2458 Planarity : 0.006 0.130 2456 Dihedral : 18.100 178.336 2839 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.13 % Allowed : 23.10 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1731 helix: 2.06 (0.16), residues: 1055 sheet: -0.51 (0.47), residues: 122 loop : -0.78 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 438 HIS 0.007 0.001 HIS A 113 PHE 0.016 0.002 PHE A 599 TYR 0.022 0.002 TYR D 109 ARG 0.005 0.000 ARG D 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 696 GLU cc_start: 0.7735 (tp30) cc_final: 0.7359 (tt0) REVERT: A 1012 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6749 (m-70) REVERT: A 1599 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8342 (tt) REVERT: A 1611 PHE cc_start: 0.7741 (m-80) cc_final: 0.7257 (m-80) REVERT: A 1618 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7437 (pp30) REVERT: D 102 PHE cc_start: 0.8986 (t80) cc_final: 0.8673 (t80) REVERT: D 159 GLN cc_start: 0.8922 (tt0) cc_final: 0.8438 (tm-30) outliers start: 30 outliers final: 19 residues processed: 138 average time/residue: 0.2831 time to fit residues: 58.8126 Evaluate side-chains 132 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1599 LEU Chi-restraints excluded: chain A residue 1618 GLN Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 173 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN A 445 GLN ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 15220 Z= 0.354 Angle : 0.745 14.598 20923 Z= 0.400 Chirality : 0.042 0.257 2458 Planarity : 0.006 0.139 2456 Dihedral : 18.083 177.501 2839 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 3.13 % Allowed : 22.74 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1731 helix: 1.89 (0.16), residues: 1056 sheet: -0.55 (0.47), residues: 121 loop : -0.78 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 438 HIS 0.007 0.001 HIS A 113 PHE 0.023 0.002 PHE A 599 TYR 0.015 0.002 TYR A 838 ARG 0.003 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 113 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6489 (mtp180) REVERT: A 696 GLU cc_start: 0.7839 (tp30) cc_final: 0.7271 (tt0) REVERT: A 789 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8562 (mt) REVERT: A 1012 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.6804 (m-70) REVERT: A 1599 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8261 (tt) REVERT: A 1618 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7568 (pp30) REVERT: D 102 PHE cc_start: 0.8921 (t80) cc_final: 0.8592 (t80) REVERT: D 159 GLN cc_start: 0.8957 (tt0) cc_final: 0.8480 (tm-30) outliers start: 44 outliers final: 26 residues processed: 149 average time/residue: 0.2814 time to fit residues: 63.0289 Evaluate side-chains 137 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1419 SER Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1535 ASN Chi-restraints excluded: chain A residue 1599 LEU Chi-restraints excluded: chain D residue 173 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.0040 chunk 110 optimal weight: 0.3980 chunk 165 optimal weight: 30.0000 chunk 174 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN A 686 ASN ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15220 Z= 0.182 Angle : 0.683 12.977 20923 Z= 0.373 Chirality : 0.039 0.260 2458 Planarity : 0.006 0.127 2456 Dihedral : 17.959 178.151 2839 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.99 % Allowed : 23.17 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.21), residues: 1731 helix: 2.07 (0.16), residues: 1055 sheet: -0.54 (0.47), residues: 122 loop : -0.76 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 70 HIS 0.007 0.001 HIS A 113 PHE 0.021 0.001 PHE D 187 TYR 0.014 0.001 TYR A 838 ARG 0.002 0.000 ARG A1363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6479 (mtp180) REVERT: C 75 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7781 (mtt180) REVERT: A 696 GLU cc_start: 0.7809 (tp30) cc_final: 0.7434 (tt0) REVERT: A 789 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8550 (mt) REVERT: A 1012 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.6775 (m-70) REVERT: A 1599 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8331 (tt) REVERT: A 1618 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7607 (pp30) REVERT: D 159 GLN cc_start: 0.8955 (tt0) cc_final: 0.8492 (tm-30) outliers start: 42 outliers final: 27 residues processed: 146 average time/residue: 0.2966 time to fit residues: 64.0813 Evaluate side-chains 145 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1535 ASN Chi-restraints excluded: chain A residue 1599 LEU Chi-restraints excluded: chain A residue 1618 GLN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 190 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.143 15220 Z= 0.712 Angle : 0.905 19.548 20923 Z= 0.473 Chirality : 0.052 0.323 2458 Planarity : 0.007 0.150 2456 Dihedral : 18.365 171.735 2839 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 3.77 % Allowed : 22.96 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1731 helix: 1.50 (0.16), residues: 1047 sheet: -0.78 (0.47), residues: 121 loop : -0.94 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 435 HIS 0.009 0.002 HIS A 113 PHE 0.034 0.003 PHE A 599 TYR 0.025 0.003 TYR C 88 ARG 0.008 0.001 ARG A 819 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 110 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 807 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7543 (p0) REVERT: A 1012 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.6913 (m-70) REVERT: A 1334 PHE cc_start: 0.7669 (m-10) cc_final: 0.7430 (m-10) REVERT: A 1599 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8375 (tt) REVERT: D 159 GLN cc_start: 0.9013 (tt0) cc_final: 0.8534 (tm-30) outliers start: 53 outliers final: 36 residues processed: 153 average time/residue: 0.2827 time to fit residues: 64.2842 Evaluate side-chains 146 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 107 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1419 SER Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1438 LEU Chi-restraints excluded: chain A residue 1535 ASN Chi-restraints excluded: chain A residue 1599 LEU Chi-restraints excluded: chain D residue 101 ARG Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 190 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 175 optimal weight: 0.0670 chunk 145 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15220 Z= 0.173 Angle : 0.693 12.953 20923 Z= 0.380 Chirality : 0.039 0.258 2458 Planarity : 0.006 0.124 2456 Dihedral : 18.081 178.049 2839 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.84 % Allowed : 24.09 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1731 helix: 1.91 (0.16), residues: 1062 sheet: -0.70 (0.46), residues: 122 loop : -0.86 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 498 HIS 0.008 0.001 HIS A 113 PHE 0.017 0.001 PHE A 526 TYR 0.019 0.001 TYR A1432 ARG 0.005 0.000 ARG A1358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6428 (mtp180) REVERT: C 75 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7881 (mtt180) REVERT: A 172 ASN cc_start: 0.8294 (t0) cc_final: 0.7897 (m110) REVERT: A 696 GLU cc_start: 0.7842 (tp30) cc_final: 0.7397 (tt0) REVERT: A 1012 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.6892 (m-70) REVERT: A 1363 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7983 (mtp85) REVERT: A 1599 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8236 (tt) REVERT: A 1618 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7831 (pp30) REVERT: D 159 GLN cc_start: 0.8985 (tt0) cc_final: 0.8551 (tm-30) outliers start: 40 outliers final: 23 residues processed: 136 average time/residue: 0.2904 time to fit residues: 58.4039 Evaluate side-chains 131 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1535 ASN Chi-restraints excluded: chain A residue 1599 LEU Chi-restraints excluded: chain A residue 1618 GLN Chi-restraints excluded: chain D residue 101 ARG Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 190 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 9.9990 chunk 19 optimal weight: 0.0040 chunk 99 optimal weight: 0.5980 chunk 127 optimal weight: 30.0000 chunk 147 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15220 Z= 0.177 Angle : 0.690 12.612 20923 Z= 0.377 Chirality : 0.039 0.258 2458 Planarity : 0.006 0.126 2456 Dihedral : 17.924 179.229 2839 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.84 % Allowed : 23.38 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.21), residues: 1731 helix: 2.04 (0.16), residues: 1062 sheet: -0.59 (0.47), residues: 122 loop : -0.77 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 438 HIS 0.007 0.001 HIS A 113 PHE 0.013 0.001 PHE A 526 TYR 0.018 0.001 TYR A 837 ARG 0.007 0.000 ARG A1358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 108 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6415 (mtp180) REVERT: C 75 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7796 (mtt180) REVERT: A 172 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7881 (m110) REVERT: A 696 GLU cc_start: 0.7843 (tp30) cc_final: 0.7410 (tt0) REVERT: A 873 LYS cc_start: 0.7250 (tppt) cc_final: 0.6909 (tmtt) REVERT: A 1012 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6861 (m-70) REVERT: A 1363 ARG cc_start: 0.8309 (mtp180) cc_final: 0.8062 (mtp85) REVERT: A 1618 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7894 (pp30) REVERT: D 106 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8850 (mp10) REVERT: D 159 GLN cc_start: 0.8989 (tt0) cc_final: 0.8553 (tm-30) outliers start: 40 outliers final: 29 residues processed: 138 average time/residue: 0.3085 time to fit residues: 61.4146 Evaluate side-chains 139 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 778 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1535 ASN Chi-restraints excluded: chain D residue 101 ARG Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 190 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 0.0170 chunk 118 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 overall best weight: 0.5832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN C 330 GLN ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15220 Z= 0.167 Angle : 0.683 12.625 20923 Z= 0.374 Chirality : 0.039 0.282 2458 Planarity : 0.006 0.124 2456 Dihedral : 17.834 179.769 2839 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.20 % Allowed : 22.96 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1731 helix: 2.08 (0.16), residues: 1061 sheet: -0.50 (0.47), residues: 122 loop : -0.74 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 185 HIS 0.007 0.001 HIS A 113 PHE 0.013 0.001 PHE A 526 TYR 0.019 0.001 TYR A 837 ARG 0.007 0.000 ARG A1598 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 106 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6426 (mtp180) REVERT: C 75 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7793 (mtt180) REVERT: A 172 ASN cc_start: 0.8209 (t0) cc_final: 0.7939 (m110) REVERT: A 696 GLU cc_start: 0.7859 (tp30) cc_final: 0.7436 (tt0) REVERT: A 873 LYS cc_start: 0.7240 (tppt) cc_final: 0.6904 (tmtt) REVERT: A 1012 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.6861 (m-70) REVERT: A 1363 ARG cc_start: 0.8334 (mtp180) cc_final: 0.8085 (mtp85) REVERT: A 1410 ASP cc_start: 0.7145 (t0) cc_final: 0.6751 (t0) REVERT: A 1597 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8184 (ptmt) REVERT: A 1618 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7982 (pp30) REVERT: D 159 GLN cc_start: 0.8984 (tt0) cc_final: 0.8564 (tm-30) outliers start: 45 outliers final: 29 residues processed: 144 average time/residue: 0.2873 time to fit residues: 60.9423 Evaluate side-chains 139 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1535 ASN Chi-restraints excluded: chain A residue 1597 LYS Chi-restraints excluded: chain D residue 101 ARG Chi-restraints excluded: chain D residue 173 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 153 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15220 Z= 0.242 Angle : 0.716 13.053 20923 Z= 0.385 Chirality : 0.040 0.288 2458 Planarity : 0.006 0.131 2456 Dihedral : 17.821 178.914 2839 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.70 % Allowed : 22.96 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.21), residues: 1731 helix: 2.05 (0.16), residues: 1062 sheet: -0.47 (0.47), residues: 121 loop : -0.73 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 185 HIS 0.007 0.001 HIS A 113 PHE 0.017 0.001 PHE A 599 TYR 0.018 0.002 TYR A 837 ARG 0.005 0.000 ARG A1598 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 108 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6446 (mtp180) REVERT: A 172 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7928 (m110) REVERT: A 696 GLU cc_start: 0.7865 (tp30) cc_final: 0.7433 (tt0) REVERT: A 873 LYS cc_start: 0.7259 (tppt) cc_final: 0.6863 (tmtt) REVERT: A 1012 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.6836 (m-70) REVERT: A 1410 ASP cc_start: 0.7123 (t0) cc_final: 0.6718 (t0) REVERT: A 1597 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8155 (ptmt) REVERT: A 1618 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8007 (pp30) REVERT: D 106 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8933 (mp10) REVERT: D 159 GLN cc_start: 0.8992 (tt0) cc_final: 0.8569 (tm-30) outliers start: 38 outliers final: 32 residues processed: 137 average time/residue: 0.3008 time to fit residues: 60.2935 Evaluate side-chains 143 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1419 SER Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1535 ASN Chi-restraints excluded: chain A residue 1597 LYS Chi-restraints excluded: chain D residue 101 ARG Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 119 optimal weight: 0.0470 chunk 180 optimal weight: 0.2980 chunk 165 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15220 Z= 0.177 Angle : 0.699 13.471 20923 Z= 0.379 Chirality : 0.039 0.305 2458 Planarity : 0.006 0.124 2456 Dihedral : 17.704 179.691 2839 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.70 % Allowed : 23.17 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.21), residues: 1731 helix: 2.08 (0.16), residues: 1062 sheet: -0.44 (0.47), residues: 122 loop : -0.73 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 185 HIS 0.007 0.001 HIS A 113 PHE 0.014 0.001 PHE D 187 TYR 0.020 0.001 TYR A 837 ARG 0.005 0.000 ARG A1358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6468 (mtp180) REVERT: A 172 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7893 (m110) REVERT: A 696 GLU cc_start: 0.7838 (tp30) cc_final: 0.7418 (tt0) REVERT: A 873 LYS cc_start: 0.7200 (tppt) cc_final: 0.6831 (tmtt) REVERT: A 1012 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6893 (m-70) REVERT: A 1363 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8389 (mtp85) REVERT: A 1410 ASP cc_start: 0.7153 (t0) cc_final: 0.6750 (t0) REVERT: A 1597 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8204 (ptmt) REVERT: A 1618 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8011 (pp30) REVERT: D 106 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8940 (mp10) REVERT: D 109 TYR cc_start: 0.8222 (t80) cc_final: 0.8021 (t80) REVERT: D 159 GLN cc_start: 0.8988 (tt0) cc_final: 0.8574 (tm-30) outliers start: 38 outliers final: 30 residues processed: 139 average time/residue: 0.2968 time to fit residues: 60.4666 Evaluate side-chains 144 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 1012 HIS Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1419 SER Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1597 LYS Chi-restraints excluded: chain D residue 101 ARG Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 0.0980 chunk 60 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.142339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.114199 restraints weight = 29461.292| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.68 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15220 Z= 0.196 Angle : 0.709 12.980 20923 Z= 0.382 Chirality : 0.039 0.293 2458 Planarity : 0.006 0.125 2456 Dihedral : 17.603 179.942 2839 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.63 % Allowed : 23.24 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1731 helix: 2.08 (0.16), residues: 1062 sheet: -0.42 (0.47), residues: 122 loop : -0.74 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 185 HIS 0.007 0.001 HIS A 113 PHE 0.014 0.001 PHE A 599 TYR 0.018 0.001 TYR A 837 ARG 0.009 0.000 ARG A1358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.56 seconds wall clock time: 53 minutes 3.97 seconds (3183.97 seconds total)