Starting phenix.real_space_refine on Mon Aug 5 16:58:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/08_2024/8tx1_41674.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/08_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_41674/08_2024/8tx1_41674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/08_2024/8tx1_41674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/08_2024/8tx1_41674.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/08_2024/8tx1_41674.cif" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.83, per 1000 atoms: 0.65 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: 5.39 Conformation dependent library (CDL) restraints added in 3.2 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: 2.10 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: 6.26 Time building geometry restraints manager: 6.00 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 3.040 nonbonded pdb=" O PRO A1466 " pdb=" NZ LYS A1542 " model vdw 2.166 3.120 nonbonded pdb=" OG1 THR A 398 " pdb=" OD1 ASP A 400 " model vdw 2.203 3.040 nonbonded pdb=" O PRO A1484 " pdb=" OG1 THR A1555 " model vdw 2.225 3.040 nonbonded pdb=" O LYS A1567 " pdb=" OG1 THR A1570 " model vdw 2.237 3.040 ... (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: 3.130 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 43.430 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.360 ------------------------------------------------------------------------------- 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 : 1.541 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: 0.2092 time to fit residues: 25.2934 Evaluate side-chains 66 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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: 7.9990 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 0.0000 chunk 76 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 0.0670 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 overall best weight: 2.2126 ------------------------------------------------------------------------------- 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 311 ASN A1061 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1637 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5230 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14067 Z= 0.240 Angle : 0.646 8.888 19393 Z= 0.323 Chirality : 0.043 0.173 2303 Planarity : 0.006 0.081 2537 Dihedral : 4.588 36.662 2016 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.53 % Favored : 93.21 % Rotamer: Outliers : 3.90 % Allowed : 27.28 % Favored : 68.82 % 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: 0.03 (0.20), residues: 1884 helix: 1.22 (0.63), residues: 68 sheet: 1.47 (0.26), residues: 382 loop : -0.48 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 420 HIS 0.003 0.002 HIS A 411 PHE 0.018 0.001 PHE A1538 TYR 0.021 0.001 TYR A1208 ARG 0.008 0.001 ARG A1242 *********************** 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 135 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 77 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 833 PHE cc_start: 0.8235 (m-80) cc_final: 0.7906 (m-10) REVERT: A 966 MET cc_start: -0.2047 (mtm) cc_final: -0.2366 (mtm) REVERT: A 1101 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6693 (mmp) REVERT: A 1229 ILE cc_start: 0.2747 (OUTLIER) cc_final: 0.2224 (tp) REVERT: A 1252 ILE cc_start: 0.5441 (OUTLIER) cc_final: 0.5048 (mm) REVERT: A 1269 THR cc_start: 0.2536 (OUTLIER) cc_final: 0.2077 (p) REVERT: A 1421 GLN cc_start: 0.4572 (OUTLIER) cc_final: 0.2711 (mt0) REVERT: A 1480 GLN cc_start: 0.5392 (OUTLIER) cc_final: 0.3635 (tp40) outliers start: 58 outliers final: 29 residues processed: 124 average time/residue: 0.1988 time to fit residues: 40.2887 Evaluate side-chains 103 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 68 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR 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 507 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1101 MET Chi-restraints excluded: chain A residue 1128 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 1252 ILE 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 1361 CYS Chi-restraints excluded: chain A residue 1383 VAL 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 1469 THR Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1506 ASN Chi-restraints excluded: chain A residue 1588 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 142 optimal weight: 0.0070 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 185 optimal weight: 0.0020 chunk 153 optimal weight: 9.9990 chunk 170 optimal weight: 40.0000 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 overall best weight: 1.4008 ------------------------------------------------------------------------------- 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** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5222 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14067 Z= 0.184 Angle : 0.591 7.739 19393 Z= 0.293 Chirality : 0.042 0.206 2303 Planarity : 0.005 0.074 2537 Dihedral : 4.220 25.263 2013 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.42 % Favored : 93.31 % Rotamer: Outliers : 4.03 % Allowed : 27.55 % Favored : 68.41 % 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: 0.01 (0.20), residues: 1884 helix: 1.41 (0.64), residues: 68 sheet: 1.35 (0.26), residues: 382 loop : -0.47 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 420 HIS 0.003 0.001 HIS A1272 PHE 0.014 0.001 PHE A1538 TYR 0.013 0.001 TYR A1226 ARG 0.006 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: 60 poor density : 77 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.2455 (OUTLIER) cc_final: -0.3001 (m-80) REVERT: A 833 PHE cc_start: 0.8244 (m-80) cc_final: 0.7928 (m-10) REVERT: A 966 MET cc_start: -0.2082 (mtm) cc_final: -0.2395 (mtm) REVERT: A 1421 GLN cc_start: 0.4844 (OUTLIER) cc_final: 0.3342 (tt0) REVERT: A 1427 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6945 (mm) REVERT: A 1747 CYS cc_start: 0.3514 (OUTLIER) cc_final: 0.2849 (p) outliers start: 60 outliers final: 35 residues processed: 125 average time/residue: 0.2053 time to fit residues: 42.0724 Evaluate side-chains 107 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 68 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 205 SER 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 354 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 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 1052 CYS Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1270 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 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP 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 1453 TYR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1747 CYS 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: 30.0000 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN A1058 GLN ** A1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 14067 Z= 0.431 Angle : 0.848 12.342 19393 Z= 0.441 Chirality : 0.049 0.241 2303 Planarity : 0.008 0.103 2537 Dihedral : 6.136 32.802 2013 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.60 % Favored : 91.03 % Rotamer: Outliers : 5.24 % Allowed : 27.15 % Favored : 67.61 % 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: -0.87 (0.19), residues: 1884 helix: -0.07 (0.59), residues: 74 sheet: 0.69 (0.26), residues: 384 loop : -1.04 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A1236 HIS 0.016 0.004 HIS A 411 PHE 0.026 0.003 PHE A1538 TYR 0.039 0.003 TYR A1453 ARG 0.010 0.001 ARG A1242 *********************** 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 149 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 71 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.1898 (OUTLIER) cc_final: -0.2386 (m-80) REVERT: A 753 ILE cc_start: 0.6087 (OUTLIER) cc_final: 0.5754 (pt) REVERT: A 953 TYR cc_start: 0.3844 (m-10) cc_final: 0.3545 (m-10) REVERT: A 1101 MET cc_start: 0.6874 (mmp) cc_final: 0.6430 (mmp) REVERT: A 1229 ILE cc_start: 0.3301 (OUTLIER) cc_final: 0.2943 (tp) REVERT: A 1252 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6366 (mm) REVERT: A 1421 GLN cc_start: 0.5586 (OUTLIER) cc_final: 0.3579 (mt0) REVERT: A 1453 TYR cc_start: 0.5761 (OUTLIER) cc_final: 0.4528 (t80) REVERT: A 1747 CYS cc_start: 0.3668 (OUTLIER) cc_final: 0.2941 (p) outliers start: 78 outliers final: 45 residues processed: 137 average time/residue: 0.2006 time to fit residues: 44.4278 Evaluate side-chains 115 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 63 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 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 317 VAL 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 594 CYS Chi-restraints excluded: chain A residue 619 THR 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 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 952 TYR 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 1109 SER Chi-restraints excluded: chain A residue 1128 VAL 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 1252 ILE Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1318 THR 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 1453 TYR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1584 THR Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1609 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 46 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN A 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14067 Z= 0.312 Angle : 0.721 9.505 19393 Z= 0.368 Chirality : 0.045 0.234 2303 Planarity : 0.007 0.086 2537 Dihedral : 5.711 29.868 2013 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.59 % Favored : 92.09 % Rotamer: Outliers : 5.11 % Allowed : 27.96 % Favored : 66.94 % 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: -1.06 (0.19), residues: 1884 helix: 0.18 (0.60), residues: 74 sheet: 0.45 (0.26), residues: 376 loop : -1.16 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 771 HIS 0.009 0.003 HIS A1276 PHE 0.022 0.002 PHE A 961 TYR 0.024 0.002 TYR A1453 ARG 0.007 0.001 ARG A1179 *********************** 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 141 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 65 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.2240 (OUTLIER) cc_final: -0.2664 (m-80) REVERT: A 1229 ILE cc_start: 0.2790 (OUTLIER) cc_final: 0.2422 (tp) REVERT: A 1421 GLN cc_start: 0.5512 (OUTLIER) cc_final: 0.3736 (mt0) REVERT: A 1436 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7196 (p) REVERT: A 1453 TYR cc_start: 0.5979 (OUTLIER) cc_final: 0.5410 (m-80) REVERT: A 1480 GLN cc_start: 0.5243 (OUTLIER) cc_final: 0.3107 (tp40) REVERT: A 1747 CYS cc_start: 0.3435 (OUTLIER) cc_final: 0.2516 (p) REVERT: A 1981 MET cc_start: 0.3640 (OUTLIER) cc_final: 0.3300 (ptt) outliers start: 76 outliers final: 45 residues processed: 130 average time/residue: 0.1833 time to fit residues: 39.5689 Evaluate side-chains 113 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 60 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 57 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 354 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 662 PHE Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 854 VAL 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 1052 CYS 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 1172 VAL 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 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 1418 PHE 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 1436 THR Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1609 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14067 Z= 0.296 Angle : 0.707 8.659 19393 Z= 0.360 Chirality : 0.045 0.230 2303 Planarity : 0.007 0.085 2537 Dihedral : 5.644 29.436 2013 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.86 % Favored : 90.82 % Rotamer: Outliers : 5.44 % Allowed : 27.96 % Favored : 66.60 % 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: -1.15 (0.19), residues: 1884 helix: 0.24 (0.61), residues: 74 sheet: 0.31 (0.27), residues: 382 loop : -1.22 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 771 HIS 0.010 0.003 HIS A1276 PHE 0.018 0.002 PHE A1418 TYR 0.027 0.002 TYR A1453 ARG 0.004 0.000 ARG A1712 *********************** 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 149 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 68 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 TYR cc_start: 0.0283 (OUTLIER) cc_final: -0.0227 (m-10) REVERT: A 662 PHE cc_start: -0.2459 (OUTLIER) cc_final: -0.2868 (m-80) REVERT: A 833 PHE cc_start: 0.7814 (m-80) cc_final: 0.7600 (m-10) REVERT: A 1101 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6424 (mmp) REVERT: A 1227 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.5020 (mtt-85) REVERT: A 1229 ILE cc_start: 0.2981 (OUTLIER) cc_final: 0.2500 (tp) REVERT: A 1421 GLN cc_start: 0.5507 (OUTLIER) cc_final: 0.3683 (mt0) REVERT: A 1436 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7245 (p) REVERT: A 1453 TYR cc_start: 0.5619 (OUTLIER) cc_final: 0.4736 (m-80) REVERT: A 1480 GLN cc_start: 0.5272 (OUTLIER) cc_final: 0.3074 (tp40) REVERT: A 1747 CYS cc_start: 0.3367 (OUTLIER) cc_final: 0.2488 (p) REVERT: A 1981 MET cc_start: 0.3509 (OUTLIER) cc_final: 0.2947 (ptt) outliers start: 81 outliers final: 51 residues processed: 138 average time/residue: 0.2030 time to fit residues: 45.5251 Evaluate side-chains 124 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 62 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 142 LEU Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 421 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 594 CYS Chi-restraints excluded: chain A residue 599 THR 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 791 GLN Chi-restraints excluded: chain A residue 844 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 1073 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1101 MET Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1135 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 1227 ARG 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 1300 VAL 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 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1453 TYR 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 1609 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 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: 20.0000 chunk 20 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 182 optimal weight: 0.2980 chunk 114 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14067 Z= 0.191 Angle : 0.629 9.049 19393 Z= 0.314 Chirality : 0.042 0.173 2303 Planarity : 0.006 0.082 2537 Dihedral : 4.970 25.528 2013 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.53 % Favored : 93.15 % Rotamer: Outliers : 3.49 % Allowed : 29.57 % Favored : 66.94 % 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: -0.89 (0.19), residues: 1884 helix: 0.97 (0.64), residues: 68 sheet: 0.46 (0.27), residues: 382 loop : -1.04 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 771 HIS 0.008 0.002 HIS A 847 PHE 0.017 0.001 PHE A1308 TYR 0.019 0.001 TYR A 385 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 118 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 66 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6046 (m-10) REVERT: A 306 LEU cc_start: 0.4593 (OUTLIER) cc_final: 0.4130 (mt) REVERT: A 606 TYR cc_start: -0.0026 (OUTLIER) cc_final: -0.0457 (m-10) REVERT: A 662 PHE cc_start: -0.2850 (OUTLIER) cc_final: -0.3217 (m-80) REVERT: A 792 MET cc_start: -0.0566 (mtm) cc_final: -0.1213 (mtm) REVERT: A 833 PHE cc_start: 0.7771 (m-80) cc_final: 0.7546 (m-10) REVERT: A 1271 TYR cc_start: 0.3632 (m-80) cc_final: 0.3359 (m-80) REVERT: A 1480 GLN cc_start: 0.5247 (OUTLIER) cc_final: 0.3236 (tp40) REVERT: A 1747 CYS cc_start: 0.3241 (OUTLIER) cc_final: 0.2357 (p) REVERT: A 1981 MET cc_start: 0.2927 (OUTLIER) cc_final: 0.2457 (ptt) outliers start: 52 outliers final: 36 residues processed: 114 average time/residue: 0.2052 time to fit residues: 38.6242 Evaluate side-chains 100 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 57 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 175 PHE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 LEU 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 606 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1109 SER 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 1300 VAL 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 1418 PHE 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 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 1557 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG 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: 0.0980 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 0.4980 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 moved from start: 0.3754 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= 0.177 Angle : 0.600 9.792 19393 Z= 0.295 Chirality : 0.042 0.161 2303 Planarity : 0.006 0.075 2537 Dihedral : 4.516 22.438 2013 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.17 % Favored : 92.57 % Rotamer: Outliers : 3.09 % Allowed : 29.70 % Favored : 67.20 % 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: -0.75 (0.19), residues: 1884 helix: 1.19 (0.65), residues: 68 sheet: 0.66 (0.27), residues: 380 loop : -0.98 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1417 HIS 0.006 0.001 HIS A 847 PHE 0.010 0.001 PHE A1308 TYR 0.016 0.001 TYR A1029 ARG 0.003 0.000 ARG A1712 *********************** 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 110 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 64 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6084 (m-10) REVERT: A 606 TYR cc_start: 0.0148 (OUTLIER) cc_final: -0.0293 (m-10) REVERT: A 662 PHE cc_start: -0.2720 (OUTLIER) cc_final: -0.3153 (m-80) REVERT: A 1229 ILE cc_start: 0.2882 (OUTLIER) cc_final: 0.2439 (tp) REVERT: A 1271 TYR cc_start: 0.3589 (m-80) cc_final: 0.3341 (m-80) REVERT: A 1480 GLN cc_start: 0.5171 (OUTLIER) cc_final: 0.3203 (tp40) REVERT: A 1747 CYS cc_start: 0.3192 (OUTLIER) cc_final: 0.2269 (p) outliers start: 46 outliers final: 34 residues processed: 106 average time/residue: 0.1925 time to fit residues: 34.3078 Evaluate side-chains 100 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 60 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 175 PHE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 421 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 606 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1073 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 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1361 CYS Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL 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 1557 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 1981 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 160 optimal weight: 40.0000 chunk 111 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A1421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 14067 Z= 0.381 Angle : 0.772 9.633 19393 Z= 0.396 Chirality : 0.047 0.228 2303 Planarity : 0.007 0.077 2537 Dihedral : 5.721 32.439 2013 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.55 % Favored : 90.13 % Rotamer: Outliers : 3.70 % Allowed : 29.30 % Favored : 67.00 % 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: -1.13 (0.19), residues: 1884 helix: 0.17 (0.60), residues: 74 sheet: 0.41 (0.27), residues: 364 loop : -1.20 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1236 HIS 0.017 0.004 HIS A1276 PHE 0.022 0.002 PHE A1538 TYR 0.031 0.002 TYR A1453 ARG 0.006 0.001 ARG A1036 *********************** 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 112 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 57 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.5993 (m-10) REVERT: A 306 LEU cc_start: 0.4515 (OUTLIER) cc_final: 0.4124 (mt) REVERT: A 606 TYR cc_start: 0.0245 (OUTLIER) cc_final: -0.0248 (m-10) REVERT: A 662 PHE cc_start: -0.2526 (OUTLIER) cc_final: -0.2876 (m-80) REVERT: A 1227 ARG cc_start: 0.5880 (OUTLIER) cc_final: 0.5579 (mtt-85) REVERT: A 1229 ILE cc_start: 0.3312 (OUTLIER) cc_final: 0.2951 (tp) REVERT: A 1747 CYS cc_start: 0.3294 (OUTLIER) cc_final: 0.2522 (p) REVERT: A 1981 MET cc_start: 0.3703 (OUTLIER) cc_final: 0.3080 (ptt) outliers start: 55 outliers final: 36 residues processed: 107 average time/residue: 0.1964 time to fit residues: 34.9544 Evaluate side-chains 95 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 51 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 306 LEU 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 564 THR Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR 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 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1227 ARG Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1300 VAL 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 1383 VAL Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL 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 1588 VAL Chi-restraints excluded: chain A residue 1609 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 1975 VAL 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: 0.8980 chunk 85 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 173 optimal weight: 30.0000 chunk 149 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 159 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A1421 GLN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5613 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14067 Z= 0.272 Angle : 0.697 18.021 19393 Z= 0.347 Chirality : 0.044 0.184 2303 Planarity : 0.006 0.083 2537 Dihedral : 5.458 25.929 2013 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.01 % Favored : 91.67 % Rotamer: Outliers : 3.02 % Allowed : 30.17 % Favored : 66.80 % 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: -1.12 (0.19), residues: 1884 helix: 0.39 (0.61), residues: 74 sheet: 0.32 (0.27), residues: 364 loop : -1.18 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 771 HIS 0.010 0.003 HIS A1276 PHE 0.016 0.001 PHE A1538 TYR 0.020 0.002 TYR A 385 ARG 0.004 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 93 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 48 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5871 (m-10) REVERT: A 306 LEU cc_start: 0.4374 (OUTLIER) cc_final: 0.3984 (mt) REVERT: A 606 TYR cc_start: -0.0070 (OUTLIER) cc_final: -0.0562 (m-10) REVERT: A 662 PHE cc_start: -0.2733 (OUTLIER) cc_final: -0.3100 (m-80) REVERT: A 833 PHE cc_start: 0.8079 (m-80) cc_final: 0.7855 (m-10) REVERT: A 1101 MET cc_start: 0.6499 (mmp) cc_final: 0.6298 (mmp) REVERT: A 1227 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.5555 (mtt-85) REVERT: A 1229 ILE cc_start: 0.2772 (OUTLIER) cc_final: 0.2344 (tp) REVERT: A 1271 TYR cc_start: 0.3931 (m-80) cc_final: 0.3679 (m-80) REVERT: A 1480 GLN cc_start: 0.5139 (OUTLIER) cc_final: 0.2949 (tp40) REVERT: A 1497 MET cc_start: 0.7628 (mpp) cc_final: 0.7151 (mmm) REVERT: A 1747 CYS cc_start: 0.3145 (OUTLIER) cc_final: 0.2361 (p) REVERT: A 1981 MET cc_start: 0.3584 (OUTLIER) cc_final: 0.3022 (ptt) outliers start: 45 outliers final: 33 residues processed: 91 average time/residue: 0.2147 time to fit residues: 31.8191 Evaluate side-chains 91 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 49 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 306 LEU 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 564 THR Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1073 VAL 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 1227 ARG Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1300 VAL 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 1418 PHE Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL 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 1588 VAL Chi-restraints excluded: chain A residue 1609 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 1975 VAL 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: 3.9990 chunk 138 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 131 optimal weight: 0.1980 chunk 8 optimal weight: 8.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A1421 GLN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.134754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.120468 restraints weight = 93603.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.119019 restraints weight = 88393.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.119334 restraints weight = 76633.731| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14067 Z= 0.270 Angle : 0.697 16.752 19393 Z= 0.346 Chirality : 0.044 0.179 2303 Planarity : 0.006 0.081 2537 Dihedral : 5.398 28.819 2013 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.92 % Favored : 90.76 % Rotamer: Outliers : 3.23 % Allowed : 29.97 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.16 (0.19), residues: 1884 helix: 0.46 (0.62), residues: 74 sheet: 0.22 (0.27), residues: 366 loop : -1.19 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1397 HIS 0.010 0.003 HIS A1276 PHE 0.015 0.002 PHE A1538 TYR 0.019 0.002 TYR A 385 ARG 0.004 0.001 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2457.04 seconds wall clock time: 45 minutes 16.82 seconds (2716.82 seconds total)