Starting phenix.real_space_refine on Sat Mar 16 04:24:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/03_2024/8tx1_41674.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/03_2024/8tx1_41674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/03_2024/8tx1_41674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/03_2024/8tx1_41674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/03_2024/8tx1_41674.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/03_2024/8tx1_41674.pdb" } resolution = 3.62 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= 0.002 sd= 0.092 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: 4 Type Number sf(0) Gaussians S 83 5.16 5 C 8643 2.51 5 N 2234 2.21 5 O 2727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1187": "OE1" <-> "OE2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1239": "OE1" <-> "OE2" Residue "A TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1328": "OD1" <-> "OD2" Residue "A ASP 1342": "OD1" <-> "OD2" Residue "A TYR 1366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1393": "OE1" <-> "OE2" Residue "A PHE 1426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1507": "OD1" <-> "OD2" Residue "A PHE 1537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1575": "OD1" <-> "OD2" Residue "A TYR 1594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1628": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13687 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1894, 13687 Classifications: {'peptide': 1894} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 4, 'PTRANS': 195, 'TRANS': 1694} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 7.33, per 1000 atoms: 0.54 Number of scatterers: 13687 At special positions: 0 Unit cell: (114.38, 113.05, 400.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 83 16.00 O 2727 8.00 N 2234 7.00 C 8643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 594 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 790 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 905 " - pdb=" SG CYS A 947 " distance=2.03 Simple disulfide: pdb=" SG CYS A1052 " - pdb=" SG CYS A1110 " distance=2.05 Simple disulfide: pdb=" SG CYS A1182 " - pdb=" SG CYS A1213 " distance=2.03 Simple disulfide: pdb=" SG CYS A1216 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1247 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1287 " - pdb=" SG CYS A1301 " distance=2.03 Simple disulfide: pdb=" SG CYS A1304 " - pdb=" SG CYS A1317 " distance=2.02 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1358 " distance=2.03 Simple disulfide: pdb=" SG CYS A1361 " - pdb=" SG CYS A1389 " distance=2.03 Simple disulfide: pdb=" SG CYS A1392 " - pdb=" SG CYS A1405 " distance=2.03 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1445 " distance=2.03 Simple disulfide: pdb=" SG CYS A1448 " - pdb=" SG CYS A1462 " distance=2.03 Simple disulfide: pdb=" SG CYS A1465 " - pdb=" SG CYS A1479 " distance=2.04 Simple disulfide: pdb=" SG CYS A1482 " - pdb=" SG CYS A1546 " distance=2.03 Simple disulfide: pdb=" SG CYS A1566 " - pdb=" SG CYS A1593 " distance=2.03 Simple disulfide: pdb=" SG CYS A1596 " - pdb=" SG CYS A1610 " distance=2.03 Simple disulfide: pdb=" SG CYS A1613 " - pdb=" SG CYS A1627 " distance=2.03 Simple disulfide: pdb=" SG CYS A1666 " - pdb=" SG CYS A1680 " distance=2.03 Simple disulfide: pdb=" SG CYS A1683 " - pdb=" SG CYS A1697 " distance=2.03 Simple disulfide: pdb=" SG CYS A1700 " - pdb=" SG CYS A1714 " distance=2.03 Simple disulfide: pdb=" SG CYS A1717 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS A1733 " - pdb=" SG CYS A1747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1750 " - pdb=" SG CYS A1765 " distance=2.03 Simple disulfide: pdb=" SG CYS A1768 " - pdb=" SG CYS A1794 " distance=2.03 Simple disulfide: pdb=" SG CYS A1797 " - pdb=" SG CYS A1811 " distance=2.03 Simple disulfide: pdb=" SG CYS A1814 " - pdb=" SG CYS A1837 " distance=2.03 Simple disulfide: pdb=" SG CYS A1828 " - pdb=" SG CYS A1840 " distance=2.03 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: 5.37 Conformation dependent library (CDL) restraints added in 2.7 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 39 sheets defined 4.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 547 through 557 removed outlier: 3.580A pdb=" N TRP A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 822 through 827 removed outlier: 4.035A pdb=" N THR A 825 " --> pdb=" O ALA A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1077 removed outlier: 3.757A pdb=" N PHE A1077 " --> pdb=" O TYR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1424 through 1428 removed outlier: 3.638A pdb=" N THR A1428 " --> pdb=" O PRO A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1497 removed outlier: 3.601A pdb=" N MET A1497 " --> pdb=" O ARG A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1982 removed outlier: 3.772A pdb=" N GLN A1982 " --> pdb=" O ASP A1978 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.642A pdb=" N ILE A 209 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET A 189 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 311 removed outlier: 3.979A pdb=" N LEU A 363 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 372 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 386 through 391 removed outlier: 3.765A pdb=" N ILE A 403 " --> pdb=" O ASN A 453 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 405 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 451 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 423 Processing sheet with id=AA9, first strand: chain 'A' and resid 495 through 501 Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 534 removed outlier: 4.073A pdb=" N GLU A 530 " --> pdb=" O ILE A 565 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 536 through 538 Processing sheet with id=AB3, first strand: chain 'A' and resid 621 through 627 Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 688 Processing sheet with id=AB5, first strand: chain 'A' and resid 751 through 758 Processing sheet with id=AB6, first strand: chain 'A' and resid 786 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 830 through 840 removed outlier: 7.036A pdb=" N ASP A 840 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 864 through 870 Processing sheet with id=AB9, first strand: chain 'A' and resid 904 through 908 Processing sheet with id=AC1, first strand: chain 'A' and resid 1006 through 1013 removed outlier: 5.899A pdb=" N VAL A1008 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A1035 " --> pdb=" O VAL A1008 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1101 removed outlier: 4.488A pdb=" N GLN A1049 " --> pdb=" O TYR A1131 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL A1128 " --> pdb=" O ASN A1139 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASN A1139 " --> pdb=" O VAL A1128 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU A1130 " --> pdb=" O GLY A1137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1187 through 1191 Processing sheet with id=AC4, first strand: chain 'A' and resid 1302 through 1303 removed outlier: 7.371A pdb=" N TYR A1291 " --> pdb=" O ALA A1314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1308 through 1309 Processing sheet with id=AC6, first strand: chain 'A' and resid 1324 through 1327 Processing sheet with id=AC7, first strand: chain 'A' and resid 1421 through 1422 removed outlier: 3.549A pdb=" N GLN A1421 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1452 through 1453 removed outlier: 3.543A pdb=" N LEU A1463 " --> pdb=" O TYR A1453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1469 through 1470 Processing sheet with id=AD1, first strand: chain 'A' and resid 1486 through 1487 Processing sheet with id=AD2, first strand: chain 'A' and resid 1570 through 1571 removed outlier: 3.703A pdb=" N TYR A1594 " --> pdb=" O PHE A1571 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1600 through 1601 Processing sheet with id=AD4, first strand: chain 'A' and resid 1617 through 1618 removed outlier: 3.597A pdb=" N GLU A1628 " --> pdb=" O PHE A1618 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1634 through 1635 removed outlier: 3.918A pdb=" N THR A1664 " --> pdb=" O PHE A1635 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1645 through 1647 Processing sheet with id=AD7, first strand: chain 'A' and resid 1670 through 1671 Processing sheet with id=AD8, first strand: chain 'A' and resid 1704 through 1705 Processing sheet with id=AD9, first strand: chain 'A' and resid 1721 through 1722 Processing sheet with id=AE1, first strand: chain 'A' and resid 1754 through 1755 removed outlier: 3.507A pdb=" N ARG A1766 " --> pdb=" O TYR A1755 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1772 through 1773 Processing sheet with id=AE3, first strand: chain 'A' and resid 1817 through 1818 275 hydrogen bonds defined for protein. 672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.16: 1 1.16 - 1.33: 3260 1.33 - 1.50: 5227 1.50 - 1.67: 5475 1.67 - 1.84: 104 Bond restraints: 14067 Sorted by residual: bond pdb=" CB PRO A 902 " pdb=" CG PRO A 902 " ideal model delta sigma weight residual 1.492 0.991 0.501 5.00e-02 4.00e+02 1.00e+02 bond pdb=" CG PRO A 902 " pdb=" CD PRO A 902 " ideal model delta sigma weight residual 1.503 1.276 0.227 3.40e-02 8.65e+02 4.45e+01 bond pdb=" CG PRO A1528 " pdb=" CD PRO A1528 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.09e+00 bond pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 1.492 1.621 -0.129 5.00e-02 4.00e+02 6.69e+00 bond pdb=" CB PRO A1288 " pdb=" CG PRO A1288 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.65e+00 ... (remaining 14062 not shown) Histogram of bond angle deviations from ideal: 71.58 - 88.92: 2 88.92 - 106.26: 789 106.26 - 123.60: 18150 123.60 - 140.94: 451 140.94 - 158.28: 1 Bond angle restraints: 19393 Sorted by residual: angle pdb=" N PRO A 902 " pdb=" CD PRO A 902 " pdb=" CG PRO A 902 " ideal model delta sigma weight residual 103.20 74.15 29.05 1.50e+00 4.44e-01 3.75e+02 angle pdb=" CA PRO A 902 " pdb=" CB PRO A 902 " pdb=" CG PRO A 902 " ideal model delta sigma weight residual 104.50 71.58 32.92 1.90e+00 2.77e-01 3.00e+02 angle pdb=" CB PRO A 902 " pdb=" CG PRO A 902 " pdb=" CD PRO A 902 " ideal model delta sigma weight residual 106.10 158.28 -52.18 3.20e+00 9.77e-02 2.66e+02 angle pdb=" CA PRO A 902 " pdb=" N PRO A 902 " pdb=" CD PRO A 902 " ideal model delta sigma weight residual 112.00 93.50 18.50 1.40e+00 5.10e-01 1.75e+02 angle pdb=" CA PRO A 266 " pdb=" N PRO A 266 " pdb=" CD PRO A 266 " ideal model delta sigma weight residual 112.00 102.72 9.28 1.40e+00 5.10e-01 4.39e+01 ... (remaining 19388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7379 17.71 - 35.42: 843 35.42 - 53.13: 189 53.13 - 70.84: 43 70.84 - 88.55: 15 Dihedral angle restraints: 8469 sinusoidal: 3020 harmonic: 5449 Sorted by residual: dihedral pdb=" CB CYS A1750 " pdb=" SG CYS A1750 " pdb=" SG CYS A1765 " pdb=" CB CYS A1765 " ideal model delta sinusoidal sigma weight residual -86.00 -163.97 77.97 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CB CYS A1320 " pdb=" SG CYS A1320 " pdb=" SG CYS A1358 " pdb=" CB CYS A1358 " ideal model delta sinusoidal sigma weight residual -86.00 -160.13 74.13 1 1.00e+01 1.00e-02 6.97e+01 dihedral pdb=" CB CYS A1216 " pdb=" SG CYS A1216 " pdb=" SG CYS A1228 " pdb=" CB CYS A1228 " ideal model delta sinusoidal sigma weight residual 93.00 158.21 -65.21 1 1.00e+01 1.00e-02 5.57e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1757 0.043 - 0.087: 379 0.087 - 0.130: 159 0.130 - 0.173: 7 0.173 - 0.216: 1 Chirality restraints: 2303 Sorted by residual: chirality pdb=" CA PRO A1939 " pdb=" N PRO A1939 " pdb=" C PRO A1939 " pdb=" CB PRO A1939 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A1013 " pdb=" N ILE A1013 " pdb=" C ILE A1013 " pdb=" CB ILE A1013 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA SER A1014 " pdb=" N SER A1014 " pdb=" C SER A1014 " pdb=" CB SER A1014 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 2300 not shown) Planarity restraints: 2537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 901 " 0.093 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO A 902 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A1361 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO A1362 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO A1362 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A1362 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 104 " -0.077 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A 105 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " -0.060 5.00e-02 4.00e+02 ... (remaining 2534 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 391 2.69 - 3.24: 13332 3.24 - 3.79: 20230 3.79 - 4.35: 23857 4.35 - 4.90: 39607 Nonbonded interactions: 97417 Sorted by model distance: nonbonded pdb=" OD1 ASN A1018 " pdb=" OG1 THR A1020 " model vdw 2.136 2.440 nonbonded pdb=" O PRO A1466 " pdb=" NZ LYS A1542 " model vdw 2.166 2.520 nonbonded pdb=" OG1 THR A 398 " pdb=" OD1 ASP A 400 " model vdw 2.203 2.440 nonbonded pdb=" O PRO A1484 " pdb=" OG1 THR A1555 " model vdw 2.225 2.440 nonbonded pdb=" O LYS A1567 " pdb=" OG1 THR A1570 " model vdw 2.237 2.440 ... (remaining 97412 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: 2.290 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: 11.290 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 39.650 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5104 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 0.501 14067 Z= 0.439 Angle : 0.922 52.177 19393 Z= 0.474 Chirality : 0.042 0.216 2303 Planarity : 0.008 0.125 2537 Dihedral : 15.941 88.553 4890 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.58 % Favored : 93.21 % Rotamer: Outliers : 0.20 % Allowed : 30.85 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.18 (0.20), residues: 1884 helix: 1.38 (0.63), residues: 68 sheet: 1.65 (0.26), residues: 395 loop : -0.42 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 420 HIS 0.002 0.001 HIS A 847 PHE 0.017 0.001 PHE A1538 TYR 0.021 0.001 TYR A1208 ARG 0.010 0.001 ARG A1242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 817 CYS cc_start: 0.1719 (OUTLIER) cc_final: 0.1476 (t) REVERT: A 966 MET cc_start: -0.1974 (mtm) cc_final: -0.2311 (mtm) REVERT: A 1101 MET cc_start: 0.6333 (mmp) cc_final: 0.5896 (mmp) outliers start: 3 outliers final: 1 residues processed: 73 average time/residue: 0.2189 time to fit residues: 26.2155 Evaluate side-chains 66 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 1394 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 40.0000 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 14067 Z= 0.500 Angle : 0.883 11.969 19393 Z= 0.462 Chirality : 0.049 0.271 2303 Planarity : 0.008 0.100 2537 Dihedral : 6.126 54.281 2016 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.60 % Favored : 91.14 % Rotamer: Outliers : 6.65 % Allowed : 27.22 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.62 (0.19), residues: 1884 helix: 0.15 (0.61), residues: 74 sheet: 0.89 (0.26), residues: 387 loop : -0.87 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1236 HIS 0.009 0.003 HIS A1276 PHE 0.028 0.003 PHE A1418 TYR 0.030 0.003 TYR A 297 ARG 0.012 0.001 ARG A1359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 71 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASN cc_start: 0.6171 (m-40) cc_final: 0.5769 (t0) REVERT: A 437 MET cc_start: 0.5160 (tpp) cc_final: 0.4920 (tpp) REVERT: A 662 PHE cc_start: -0.1874 (OUTLIER) cc_final: -0.2445 (m-80) REVERT: A 966 MET cc_start: -0.1766 (mtm) cc_final: -0.2041 (mtm) REVERT: A 1109 SER cc_start: 0.2801 (OUTLIER) cc_final: 0.2495 (p) REVERT: A 1201 VAL cc_start: 0.4033 (OUTLIER) cc_final: 0.2609 (t) REVERT: A 1229 ILE cc_start: 0.3494 (OUTLIER) cc_final: 0.3130 (tp) REVERT: A 1421 GLN cc_start: 0.5691 (OUTLIER) cc_final: 0.2998 (mt0) REVERT: A 1453 TYR cc_start: 0.5504 (OUTLIER) cc_final: 0.4376 (t80) REVERT: A 1480 GLN cc_start: 0.5353 (OUTLIER) cc_final: 0.3402 (tp40) REVERT: A 1747 CYS cc_start: 0.3967 (OUTLIER) cc_final: 0.2394 (p) outliers start: 99 outliers final: 48 residues processed: 156 average time/residue: 0.1912 time to fit residues: 49.1130 Evaluate side-chains 121 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 65 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1183 PHE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1361 CYS Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1506 ASN Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1900 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 171 optimal weight: 40.0000 chunk 185 optimal weight: 0.0000 chunk 153 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5419 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14067 Z= 0.223 Angle : 0.638 8.197 19393 Z= 0.322 Chirality : 0.043 0.225 2303 Planarity : 0.006 0.079 2537 Dihedral : 5.078 34.871 2013 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.63 % Favored : 93.10 % Rotamer: Outliers : 4.23 % Allowed : 28.97 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.53 (0.19), residues: 1884 helix: 0.88 (0.63), residues: 68 sheet: 0.87 (0.26), residues: 393 loop : -0.82 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 771 HIS 0.002 0.001 HIS A1272 PHE 0.027 0.001 PHE A 961 TYR 0.025 0.001 TYR A1453 ARG 0.005 0.000 ARG A1242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 74 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASN cc_start: 0.6011 (OUTLIER) cc_final: 0.5707 (t0) REVERT: A 1201 VAL cc_start: 0.2598 (OUTLIER) cc_final: 0.0971 (t) REVERT: A 1421 GLN cc_start: 0.5540 (OUTLIER) cc_final: 0.3738 (tt0) REVERT: A 1453 TYR cc_start: 0.5136 (OUTLIER) cc_final: 0.4710 (t80) REVERT: A 1480 GLN cc_start: 0.5236 (OUTLIER) cc_final: 0.3261 (tp40) outliers start: 63 outliers final: 39 residues processed: 127 average time/residue: 0.2067 time to fit residues: 41.9484 Evaluate side-chains 109 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 65 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1183 PHE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1361 CYS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1871 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 82 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14067 Z= 0.181 Angle : 0.594 7.895 19393 Z= 0.297 Chirality : 0.042 0.198 2303 Planarity : 0.005 0.069 2537 Dihedral : 4.640 28.723 2013 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.22 % Favored : 92.57 % Rotamer: Outliers : 4.64 % Allowed : 29.23 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: -0.48 (0.20), residues: 1884 helix: 1.12 (0.64), residues: 68 sheet: 0.89 (0.26), residues: 384 loop : -0.79 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 639 HIS 0.005 0.001 HIS A 847 PHE 0.017 0.001 PHE A 961 TYR 0.011 0.001 TYR A1453 ARG 0.006 0.000 ARG A1179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 69 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.2067 (OUTLIER) cc_final: -0.2718 (m-80) REVERT: A 753 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5455 (pt) REVERT: A 1101 MET cc_start: 0.6757 (mmp) cc_final: 0.6485 (mmp) REVERT: A 1223 MET cc_start: 0.7449 (tpp) cc_final: 0.7161 (tpp) REVERT: A 1229 ILE cc_start: 0.2497 (OUTLIER) cc_final: 0.2057 (tp) REVERT: A 1421 GLN cc_start: 0.5319 (OUTLIER) cc_final: 0.3702 (tt0) REVERT: A 1453 TYR cc_start: 0.4881 (OUTLIER) cc_final: 0.4651 (t80) outliers start: 69 outliers final: 41 residues processed: 124 average time/residue: 0.1959 time to fit residues: 39.7754 Evaluate side-chains 109 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 63 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.0050 chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 136 optimal weight: 0.0470 chunk 75 optimal weight: 40.0000 chunk 155 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.0470 chunk 163 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 overall best weight: 2.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5486 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14067 Z= 0.241 Angle : 0.636 8.436 19393 Z= 0.322 Chirality : 0.042 0.186 2303 Planarity : 0.006 0.072 2537 Dihedral : 4.826 26.258 2013 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.75 % Favored : 91.93 % Rotamer: Outliers : 5.38 % Allowed : 28.56 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: -0.68 (0.19), residues: 1884 helix: 0.69 (0.63), residues: 74 sheet: 0.80 (0.26), residues: 375 loop : -0.93 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1397 HIS 0.006 0.002 HIS A1276 PHE 0.018 0.001 PHE A1091 TYR 0.022 0.002 TYR A1705 ARG 0.003 0.000 ARG A1712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 63 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.1995 (OUTLIER) cc_final: -0.2620 (m-80) REVERT: A 753 ILE cc_start: 0.5882 (OUTLIER) cc_final: 0.5527 (pt) REVERT: A 1229 ILE cc_start: 0.2579 (OUTLIER) cc_final: 0.2133 (tp) REVERT: A 1453 TYR cc_start: 0.5283 (OUTLIER) cc_final: 0.4489 (t80) REVERT: A 1480 GLN cc_start: 0.5173 (OUTLIER) cc_final: 0.3099 (tp40) outliers start: 80 outliers final: 53 residues processed: 129 average time/residue: 0.1967 time to fit residues: 41.7410 Evaluate side-chains 120 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 62 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1361 CYS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1424 SER Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1492 ASP Chi-restraints excluded: chain A residue 1506 ASN Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1049 GLN ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14067 Z= 0.404 Angle : 0.800 10.281 19393 Z= 0.414 Chirality : 0.048 0.252 2303 Planarity : 0.007 0.080 2537 Dihedral : 6.106 32.709 2013 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.35 % Favored : 89.33 % Rotamer: Outliers : 7.06 % Allowed : 28.09 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.26 (0.19), residues: 1884 helix: 0.03 (0.61), residues: 74 sheet: 0.33 (0.27), residues: 372 loop : -1.31 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 771 HIS 0.014 0.004 HIS A1276 PHE 0.024 0.002 PHE A 202 TYR 0.039 0.003 TYR A1453 ARG 0.006 0.001 ARG A1359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 59 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6075 (m-10) REVERT: A 306 LEU cc_start: 0.4393 (OUTLIER) cc_final: 0.3818 (mt) REVERT: A 606 TYR cc_start: 0.0400 (OUTLIER) cc_final: -0.0086 (m-10) REVERT: A 753 ILE cc_start: 0.6133 (OUTLIER) cc_final: 0.5825 (pt) REVERT: A 833 PHE cc_start: 0.7923 (m-80) cc_final: 0.7666 (m-10) REVERT: A 938 MET cc_start: 0.5783 (tmm) cc_final: 0.5049 (tmm) REVERT: A 1101 MET cc_start: 0.7033 (mmp) cc_final: 0.6684 (mmp) REVERT: A 1229 ILE cc_start: 0.3210 (OUTLIER) cc_final: 0.2865 (tp) REVERT: A 1394 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6844 (m-30) REVERT: A 1421 GLN cc_start: 0.5823 (OUTLIER) cc_final: 0.5506 (mt0) REVERT: A 1747 CYS cc_start: 0.2647 (OUTLIER) cc_final: 0.0212 (p) REVERT: A 1981 MET cc_start: 0.3828 (OUTLIER) cc_final: 0.3282 (ptt) outliers start: 105 outliers final: 65 residues processed: 156 average time/residue: 0.1900 time to fit residues: 48.9859 Evaluate side-chains 126 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 52 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1183 PHE Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1361 CYS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1424 SER Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 153 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5499 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14067 Z= 0.188 Angle : 0.627 10.942 19393 Z= 0.313 Chirality : 0.042 0.193 2303 Planarity : 0.006 0.080 2537 Dihedral : 4.988 24.891 2013 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.01 % Favored : 92.73 % Rotamer: Outliers : 4.03 % Allowed : 30.38 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: -0.97 (0.19), residues: 1884 helix: 0.61 (0.63), residues: 74 sheet: 0.44 (0.27), residues: 358 loop : -1.08 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 771 HIS 0.006 0.002 HIS A 847 PHE 0.010 0.001 PHE A 172 TYR 0.015 0.001 TYR A1453 ARG 0.004 0.000 ARG A1712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 66 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 753 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5528 (pt) REVERT: A 938 MET cc_start: 0.4810 (tmm) cc_final: 0.4168 (tmm) REVERT: A 1101 MET cc_start: 0.6977 (mmp) cc_final: 0.6727 (mmp) REVERT: A 1223 MET cc_start: 0.7232 (tpp) cc_final: 0.6850 (tpp) REVERT: A 1229 ILE cc_start: 0.2350 (OUTLIER) cc_final: 0.1970 (tp) REVERT: A 1453 TYR cc_start: 0.5265 (OUTLIER) cc_final: 0.4389 (m-80) REVERT: A 1747 CYS cc_start: 0.3312 (OUTLIER) cc_final: 0.1291 (p) REVERT: A 1981 MET cc_start: 0.2962 (OUTLIER) cc_final: 0.2490 (ptt) outliers start: 60 outliers final: 45 residues processed: 116 average time/residue: 0.2066 time to fit residues: 38.8615 Evaluate side-chains 106 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 56 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1718 ASP Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1896 SER Chi-restraints excluded: chain A residue 1900 SER Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 124 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 165 optimal weight: 50.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 14067 Z= 0.292 Angle : 0.685 11.850 19393 Z= 0.347 Chirality : 0.044 0.208 2303 Planarity : 0.006 0.077 2537 Dihedral : 5.287 28.612 2013 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.55 % Favored : 90.13 % Rotamer: Outliers : 4.77 % Allowed : 29.91 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: -1.14 (0.19), residues: 1884 helix: 0.48 (0.62), residues: 74 sheet: 0.29 (0.26), residues: 374 loop : -1.21 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 771 HIS 0.012 0.003 HIS A1276 PHE 0.015 0.002 PHE A 202 TYR 0.018 0.002 TYR A1453 ARG 0.004 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 53 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.6194 (m-10) REVERT: A 306 LEU cc_start: 0.4331 (OUTLIER) cc_final: 0.3949 (mt) REVERT: A 606 TYR cc_start: -0.0193 (OUTLIER) cc_final: -0.0682 (m-10) REVERT: A 753 ILE cc_start: 0.5962 (OUTLIER) cc_final: 0.5673 (pt) REVERT: A 792 MET cc_start: 0.0691 (mtm) cc_final: -0.0084 (mtm) REVERT: A 1101 MET cc_start: 0.7203 (mmp) cc_final: 0.6872 (mmp) REVERT: A 1223 MET cc_start: 0.7624 (tpp) cc_final: 0.7366 (tpp) REVERT: A 1229 ILE cc_start: 0.2860 (OUTLIER) cc_final: 0.2431 (tp) REVERT: A 1394 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: A 1453 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.4858 (m-80) REVERT: A 1747 CYS cc_start: 0.2840 (OUTLIER) cc_final: 0.0737 (p) REVERT: A 1981 MET cc_start: 0.3484 (OUTLIER) cc_final: 0.2902 (ptt) outliers start: 71 outliers final: 55 residues processed: 115 average time/residue: 0.1875 time to fit residues: 36.2094 Evaluate side-chains 116 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 52 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1361 CYS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1424 SER Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1718 ASP Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1896 SER Chi-restraints excluded: chain A residue 1900 SER Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 40.0000 chunk 159 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 14067 Z= 0.335 Angle : 0.758 12.497 19393 Z= 0.390 Chirality : 0.046 0.214 2303 Planarity : 0.007 0.088 2537 Dihedral : 6.081 30.881 2013 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.30 % Favored : 89.44 % Rotamer: Outliers : 4.37 % Allowed : 30.11 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.52 (0.19), residues: 1884 helix: -0.02 (0.60), residues: 75 sheet: -0.07 (0.27), residues: 366 loop : -1.43 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 771 HIS 0.020 0.004 HIS A1276 PHE 0.019 0.002 PHE A1032 TYR 0.032 0.002 TYR A1453 ARG 0.007 0.001 ARG A1390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 59 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.5864 (m-10) REVERT: A 230 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6876 (mp) REVERT: A 306 LEU cc_start: 0.4313 (OUTLIER) cc_final: 0.3931 (mt) REVERT: A 606 TYR cc_start: 0.0111 (OUTLIER) cc_final: -0.0388 (m-10) REVERT: A 662 PHE cc_start: -0.2470 (OUTLIER) cc_final: -0.4321 (m-80) REVERT: A 753 ILE cc_start: 0.5903 (OUTLIER) cc_final: 0.5604 (pt) REVERT: A 792 MET cc_start: 0.1890 (mtm) cc_final: 0.0893 (mtm) REVERT: A 1090 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.5436 (t80) REVERT: A 1101 MET cc_start: 0.7603 (mmp) cc_final: 0.7394 (mmp) REVERT: A 1229 ILE cc_start: 0.3136 (OUTLIER) cc_final: 0.2759 (tp) REVERT: A 1394 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: A 1421 GLN cc_start: 0.5375 (OUTLIER) cc_final: 0.4950 (mt0) REVERT: A 1747 CYS cc_start: 0.2554 (OUTLIER) cc_final: 0.0478 (p) REVERT: A 1981 MET cc_start: 0.3796 (OUTLIER) cc_final: 0.3132 (ptt) outliers start: 65 outliers final: 45 residues processed: 115 average time/residue: 0.2015 time to fit residues: 38.4752 Evaluate side-chains 109 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 52 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 255 PRO Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1090 TYR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1424 SER Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1900 SER Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.0000 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 173 optimal weight: 50.0000 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14067 Z= 0.192 Angle : 0.638 13.219 19393 Z= 0.315 Chirality : 0.042 0.195 2303 Planarity : 0.006 0.085 2537 Dihedral : 5.087 28.366 2013 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.96 % Favored : 91.77 % Rotamer: Outliers : 3.16 % Allowed : 31.45 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: -1.22 (0.20), residues: 1884 helix: 0.64 (0.63), residues: 74 sheet: 0.03 (0.27), residues: 366 loop : -1.20 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 771 HIS 0.006 0.002 HIS A 847 PHE 0.013 0.001 PHE A 202 TYR 0.021 0.001 TYR A1029 ARG 0.005 0.000 ARG A1712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 59 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: A 606 TYR cc_start: -0.0228 (OUTLIER) cc_final: -0.0689 (m-10) REVERT: A 753 ILE cc_start: 0.5645 (OUTLIER) cc_final: 0.5381 (pt) REVERT: A 792 MET cc_start: 0.1616 (mtm) cc_final: 0.0982 (mtm) REVERT: A 1229 ILE cc_start: 0.2300 (OUTLIER) cc_final: 0.1884 (tp) REVERT: A 1282 GLU cc_start: 0.5806 (mp0) cc_final: 0.5514 (mp0) REVERT: A 1394 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6717 (m-30) REVERT: A 1747 CYS cc_start: 0.2219 (OUTLIER) cc_final: 0.0190 (p) REVERT: A 1981 MET cc_start: 0.3188 (OUTLIER) cc_final: 0.2690 (ptt) outliers start: 47 outliers final: 35 residues processed: 98 average time/residue: 0.2122 time to fit residues: 34.8200 Evaluate side-chains 96 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 54 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1718 ASP Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1900 SER Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 22 optimal weight: 0.0770 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 27 optimal weight: 0.0030 chunk 131 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 overall best weight: 1.7150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.134665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.122046 restraints weight = 94902.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.120599 restraints weight = 99756.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.121100 restraints weight = 75928.089| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5416 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14067 Z= 0.207 Angle : 0.640 12.932 19393 Z= 0.316 Chirality : 0.043 0.187 2303 Planarity : 0.006 0.082 2537 Dihedral : 4.993 26.562 2013 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.70 % Favored : 91.03 % Rotamer: Outliers : 3.29 % Allowed : 31.65 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: -1.13 (0.20), residues: 1884 helix: 0.59 (0.62), residues: 74 sheet: 0.08 (0.27), residues: 366 loop : -1.13 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 771 HIS 0.008 0.002 HIS A1276 PHE 0.011 0.001 PHE A 833 TYR 0.018 0.001 TYR A1029 ARG 0.004 0.000 ARG A1712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2470.83 seconds wall clock time: 45 minutes 56.45 seconds (2756.45 seconds total)