Starting phenix.real_space_refine on Sat Aug 23 18:33:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tx1_41674/08_2025/8tx1_41674.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tx1_41674/08_2025/8tx1_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/cci-nas-00/data/ceres_data/8tx1_41674/08_2025/8tx1_41674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tx1_41674/08_2025/8tx1_41674.map" model { file = "/net/cci-nas-00/data/ceres_data/8tx1_41674/08_2025/8tx1_41674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tx1_41674/08_2025/8tx1_41674.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 3.56, per 1000 atoms: 0.26 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 - 3.00 Amino acid : True - 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: 0.96 Conformation dependent library (CDL) restraints added in 721.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.61 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: 3.78 Time building geometry restraints manager: 1.33 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: 0.00 - 10.44: 19388 10.44 - 20.87: 2 20.87 - 31.31: 1 31.31 - 41.74: 1 41.74 - 52.18: 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: 4.580 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.790 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- 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 14098 Z= 0.202 Angle : 0.924 52.177 19455 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 : 12.70 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A1242 TYR 0.021 0.001 TYR A1208 PHE 0.017 0.001 PHE A1538 TRP 0.047 0.002 TRP A 420 HIS 0.002 0.001 HIS A 847 Details of bonding type rmsd covalent geometry : bond 0.00639 (14067) covalent geometry : angle 0.92167 (19393) SS BOND : bond 0.00375 ( 31) SS BOND : angle 1.40323 ( 62) hydrogen bonds : bond 0.11986 ( 275) hydrogen bonds : angle 5.91239 ( 672) *********************** 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 to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.314 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: 0.0824 time to fit residues: 9.8201 Evaluate side-chains 66 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.0270 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.1040 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.141500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.128542 restraints weight = 94636.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.127869 restraints weight = 103144.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.128043 restraints weight = 77394.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.128182 restraints weight = 63675.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.128252 restraints weight = 57859.527| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5044 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14098 Z= 0.149 Angle : 0.647 8.783 19455 Z= 0.323 Chirality : 0.042 0.169 2303 Planarity : 0.006 0.081 2537 Dihedral : 4.545 36.128 2016 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.48 % Favored : 93.26 % Rotamer: Outliers : 3.70 % Allowed : 27.28 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.20), residues: 1884 helix: 1.28 (0.63), residues: 68 sheet: 1.49 (0.26), residues: 382 loop : -0.48 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1242 TYR 0.021 0.001 TYR A1208 PHE 0.018 0.001 PHE A1538 TRP 0.016 0.001 TRP A 420 HIS 0.002 0.001 HIS A1272 Details of bonding type rmsd covalent geometry : bond 0.00350 (14067) covalent geometry : angle 0.64474 (19393) SS BOND : bond 0.00411 ( 31) SS BOND : angle 1.18645 ( 62) hydrogen bonds : bond 0.02600 ( 275) hydrogen bonds : angle 5.25092 ( 672) *********************** 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 131 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 76 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 966 MET cc_start: -0.1251 (mtm) cc_final: -0.1605 (mtm) REVERT: A 1101 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6710 (mmp) REVERT: A 1229 ILE cc_start: 0.2788 (OUTLIER) cc_final: 0.2261 (tp) REVERT: A 1252 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.4965 (mm) REVERT: A 1269 THR cc_start: 0.2383 (OUTLIER) cc_final: 0.1869 (p) REVERT: A 1421 GLN cc_start: 0.4699 (OUTLIER) cc_final: 0.2837 (mt0) REVERT: A 1480 GLN cc_start: 0.5417 (OUTLIER) cc_final: 0.3683 (tp40) outliers start: 55 outliers final: 25 residues processed: 121 average time/residue: 0.0708 time to fit residues: 14.3414 Evaluate side-chains 97 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR 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 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 1480 GLN 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 19 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN A1058 GLN A1061 ASN ** A1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.134921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.120497 restraints weight = 94567.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.118806 restraints weight = 103163.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.119343 restraints weight = 78105.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.119357 restraints weight = 65911.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.119394 restraints weight = 64915.092| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.125 14098 Z= 0.410 Angle : 1.031 13.145 19455 Z= 0.546 Chirality : 0.055 0.323 2303 Planarity : 0.009 0.127 2537 Dihedral : 7.107 39.090 2013 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.24 % Favored : 90.13 % Rotamer: Outliers : 7.33 % Allowed : 26.14 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.19), residues: 1884 helix: -0.70 (0.57), residues: 74 sheet: 0.45 (0.26), residues: 384 loop : -1.31 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1179 TYR 0.043 0.004 TYR A1453 PHE 0.034 0.003 PHE A1538 TRP 0.035 0.003 TRP A1236 HIS 0.016 0.004 HIS A1276 Details of bonding type rmsd covalent geometry : bond 0.00912 (14067) covalent geometry : angle 1.02362 (19393) SS BOND : bond 0.00890 ( 31) SS BOND : angle 2.42973 ( 62) hydrogen bonds : bond 0.05171 ( 275) hydrogen bonds : angle 7.40103 ( 672) *********************** 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 179 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 70 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.2425 (OUTLIER) cc_final: -0.2725 (m-80) REVERT: A 1026 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6701 (mm) REVERT: A 1101 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7065 (mmp) REVERT: A 1201 VAL cc_start: 0.3631 (OUTLIER) cc_final: 0.2258 (t) REVERT: A 1227 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.5307 (mtt180) REVERT: A 1229 ILE cc_start: 0.3484 (OUTLIER) cc_final: 0.3182 (tp) REVERT: A 1421 GLN cc_start: 0.5864 (OUTLIER) cc_final: 0.3406 (mt0) REVERT: A 1436 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7321 (p) REVERT: A 1453 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.4219 (t80) REVERT: A 1747 CYS cc_start: 0.3649 (OUTLIER) cc_final: 0.2259 (p) outliers start: 109 outliers final: 57 residues processed: 164 average time/residue: 0.0881 time to fit residues: 23.3325 Evaluate side-chains 129 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 62 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 361 LEU Chi-restraints excluded: chain A residue 370 VAL 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 673 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 791 GLN 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 867 THR Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1020 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 1101 MET 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 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 1287 CYS 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 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 1479 CYS 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 1975 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 115 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 118 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 147 optimal weight: 0.0060 chunk 62 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.138201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.123218 restraints weight = 96298.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.122237 restraints weight = 78742.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.122396 restraints weight = 64161.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.122579 restraints weight = 57606.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.122527 restraints weight = 57424.865| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5483 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14098 Z= 0.128 Angle : 0.661 7.791 19455 Z= 0.335 Chirality : 0.043 0.181 2303 Planarity : 0.006 0.088 2537 Dihedral : 5.263 27.699 2013 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.16 % Favored : 93.52 % Rotamer: Outliers : 3.49 % Allowed : 28.56 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.19), residues: 1884 helix: 0.80 (0.64), residues: 68 sheet: 0.64 (0.26), residues: 386 loop : -0.99 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1179 TYR 0.015 0.001 TYR A1453 PHE 0.015 0.001 PHE A 172 TRP 0.013 0.002 TRP A 771 HIS 0.009 0.001 HIS A 847 Details of bonding type rmsd covalent geometry : bond 0.00292 (14067) covalent geometry : angle 0.65909 (19393) SS BOND : bond 0.00460 ( 31) SS BOND : angle 1.13790 ( 62) hydrogen bonds : bond 0.02735 ( 275) hydrogen bonds : angle 5.78119 ( 672) *********************** 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 130 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 78 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 753 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5645 (pt) REVERT: A 1453 TYR cc_start: 0.5249 (OUTLIER) cc_final: 0.4732 (t80) REVERT: A 1480 GLN cc_start: 0.4999 (OUTLIER) cc_final: 0.3074 (tp40) REVERT: A 1981 MET cc_start: 0.3067 (OUTLIER) cc_final: 0.2832 (ptt) outliers start: 52 outliers final: 27 residues processed: 122 average time/residue: 0.0885 time to fit residues: 17.6597 Evaluate side-chains 94 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 241 TYR Chi-restraints excluded: chain A residue 270 VAL 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 643 ILE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1318 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 1421 GLN Chi-restraints excluded: chain A residue 1432 VAL 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 1588 VAL Chi-restraints excluded: chain A residue 1609 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 178 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.136550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.123405 restraints weight = 95914.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.121955 restraints weight = 105291.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.122292 restraints weight = 86513.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.122340 restraints weight = 64588.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.122390 restraints weight = 61437.063| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14098 Z= 0.177 Angle : 0.672 8.499 19455 Z= 0.339 Chirality : 0.044 0.163 2303 Planarity : 0.006 0.083 2537 Dihedral : 5.265 27.007 2013 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.96 % Favored : 91.72 % Rotamer: Outliers : 4.10 % Allowed : 28.43 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.19), residues: 1884 helix: 0.77 (0.64), residues: 68 sheet: 0.50 (0.26), residues: 390 loop : -1.10 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1712 TYR 0.018 0.002 TYR A1453 PHE 0.030 0.002 PHE A 961 TRP 0.012 0.002 TRP A 639 HIS 0.007 0.002 HIS A1276 Details of bonding type rmsd covalent geometry : bond 0.00402 (14067) covalent geometry : angle 0.66966 (19393) SS BOND : bond 0.00438 ( 31) SS BOND : angle 1.21532 ( 62) hydrogen bonds : bond 0.02821 ( 275) hydrogen bonds : angle 5.80283 ( 672) *********************** 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 128 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 67 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 662 PHE cc_start: -0.2229 (OUTLIER) cc_final: -0.2718 (m-80) REVERT: A 753 ILE cc_start: 0.5697 (OUTLIER) cc_final: 0.5285 (pt) REVERT: A 792 MET cc_start: 0.0168 (mtm) cc_final: -0.0498 (mtm) REVERT: A 1229 ILE cc_start: 0.2624 (OUTLIER) cc_final: 0.2302 (tp) REVERT: A 1421 GLN cc_start: 0.5602 (OUTLIER) cc_final: 0.3856 (tt0) REVERT: A 1436 THR cc_start: 0.7422 (OUTLIER) cc_final: 0.7145 (p) REVERT: A 1453 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.5411 (m-80) REVERT: A 1480 GLN cc_start: 0.5387 (OUTLIER) cc_final: 0.3388 (tp40) REVERT: A 1981 MET cc_start: 0.3358 (OUTLIER) cc_final: 0.2876 (ptt) outliers start: 61 outliers final: 37 residues processed: 119 average time/residue: 0.0932 time to fit residues: 18.2952 Evaluate side-chains 108 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 63 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 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 662 PHE 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 1014 SER 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 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 1266 ILE 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 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 1479 CYS Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1871 ARG 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 48 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 145 optimal weight: 0.0670 chunk 188 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 170 optimal weight: 40.0000 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 160 optimal weight: 10.0000 overall best weight: 1.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.136924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.121579 restraints weight = 95486.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.120350 restraints weight = 82226.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.120596 restraints weight = 70790.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.120733 restraints weight = 57393.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.120782 restraints weight = 56350.331| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5578 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14098 Z= 0.132 Angle : 0.632 9.705 19455 Z= 0.317 Chirality : 0.042 0.156 2303 Planarity : 0.006 0.078 2537 Dihedral : 5.041 25.282 2013 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.79 % Favored : 92.89 % Rotamer: Outliers : 4.50 % Allowed : 28.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.19), residues: 1884 helix: 0.88 (0.64), residues: 68 sheet: 0.58 (0.26), residues: 389 loop : -1.09 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1712 TYR 0.018 0.001 TYR A1453 PHE 0.017 0.001 PHE A 961 TRP 0.009 0.001 TRP A1397 HIS 0.006 0.002 HIS A 847 Details of bonding type rmsd covalent geometry : bond 0.00306 (14067) covalent geometry : angle 0.62896 (19393) SS BOND : bond 0.00349 ( 31) SS BOND : angle 1.26925 ( 62) hydrogen bonds : bond 0.02519 ( 275) hydrogen bonds : angle 5.60200 ( 672) *********************** 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 133 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 66 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 306 LEU cc_start: 0.4700 (OUTLIER) cc_final: 0.4269 (mt) REVERT: A 606 TYR cc_start: 0.0102 (OUTLIER) cc_final: -0.0378 (m-10) REVERT: A 662 PHE cc_start: -0.2456 (OUTLIER) cc_final: -0.2891 (m-80) REVERT: A 753 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5521 (pt) REVERT: A 1421 GLN cc_start: 0.5254 (OUTLIER) cc_final: 0.3696 (tt0) REVERT: A 1436 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.6993 (p) REVERT: A 1453 TYR cc_start: 0.5675 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: A 1480 GLN cc_start: 0.5232 (OUTLIER) cc_final: 0.3199 (tp40) REVERT: A 1747 CYS cc_start: 0.3192 (OUTLIER) cc_final: 0.2339 (p) REVERT: A 1981 MET cc_start: 0.3057 (OUTLIER) cc_final: 0.2615 (ptt) outliers start: 67 outliers final: 44 residues processed: 125 average time/residue: 0.0842 time to fit residues: 17.5954 Evaluate side-chains 114 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 60 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 67 THR 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 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 753 ILE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1014 SER 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 1108 VAL 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 1162 ILE Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL 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 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 1520 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 137 optimal weight: 0.1980 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 159 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.137274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.124145 restraints weight = 94882.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.123298 restraints weight = 87791.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.123611 restraints weight = 69701.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.123667 restraints weight = 52094.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.123692 restraints weight = 49287.034| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5322 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 14098 Z= 0.121 Angle : 0.624 9.619 19455 Z= 0.309 Chirality : 0.042 0.217 2303 Planarity : 0.005 0.075 2537 Dihedral : 4.753 23.587 2013 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.54 % Favored : 92.14 % Rotamer: Outliers : 4.03 % Allowed : 28.90 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.19), residues: 1884 helix: 1.05 (0.65), residues: 68 sheet: 0.59 (0.26), residues: 388 loop : -1.04 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1712 TYR 0.021 0.001 TYR A 385 PHE 0.013 0.001 PHE A1308 TRP 0.009 0.001 TRP A 312 HIS 0.009 0.002 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00294 (14067) covalent geometry : angle 0.62204 (19393) SS BOND : bond 0.00304 ( 31) SS BOND : angle 1.08541 ( 62) hydrogen bonds : bond 0.02337 ( 275) hydrogen bonds : angle 5.31821 ( 672) *********************** 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 122 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 62 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 606 TYR cc_start: 0.0414 (OUTLIER) cc_final: -0.0143 (m-10) REVERT: A 662 PHE cc_start: -0.2698 (OUTLIER) cc_final: -0.3139 (m-80) REVERT: A 753 ILE cc_start: 0.5705 (OUTLIER) cc_final: 0.5294 (pt) REVERT: A 1229 ILE cc_start: 0.2065 (OUTLIER) cc_final: 0.1693 (tp) REVERT: A 1421 GLN cc_start: 0.5086 (OUTLIER) cc_final: 0.3668 (tt0) REVERT: A 1436 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7069 (p) REVERT: A 1480 GLN cc_start: 0.5096 (OUTLIER) cc_final: 0.3013 (tp40) outliers start: 60 outliers final: 49 residues processed: 115 average time/residue: 0.0836 time to fit residues: 16.3329 Evaluate side-chains 120 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 64 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 67 THR 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 302 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 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 753 ILE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1135 THR 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 1266 ILE Chi-restraints excluded: chain A residue 1300 VAL 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 1394 ASP 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 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 1557 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1609 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 51 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.133694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.122163 restraints weight = 94069.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.121926 restraints weight = 94126.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.120774 restraints weight = 76050.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.120563 restraints weight = 64591.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.120701 restraints weight = 56957.056| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 14098 Z= 0.284 Angle : 0.863 11.636 19455 Z= 0.443 Chirality : 0.050 0.301 2303 Planarity : 0.007 0.089 2537 Dihedral : 6.325 34.176 2013 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.35 % Favored : 89.28 % Rotamer: Outliers : 4.97 % Allowed : 28.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.19), residues: 1884 helix: -0.21 (0.58), residues: 74 sheet: 0.12 (0.27), residues: 374 loop : -1.38 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 360 TYR 0.034 0.003 TYR A1366 PHE 0.026 0.003 PHE A1032 TRP 0.029 0.003 TRP A1236 HIS 0.022 0.005 HIS A1276 Details of bonding type rmsd covalent geometry : bond 0.00644 (14067) covalent geometry : angle 0.85828 (19393) SS BOND : bond 0.00892 ( 31) SS BOND : angle 1.80376 ( 62) hydrogen bonds : bond 0.03812 ( 275) hydrogen bonds : angle 6.76099 ( 672) *********************** 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 142 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 68 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.5988 (m-10) REVERT: A 306 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.4247 (mt) REVERT: A 606 TYR cc_start: 0.0912 (OUTLIER) cc_final: 0.0200 (m-10) REVERT: A 662 PHE cc_start: -0.2530 (OUTLIER) cc_final: -0.2830 (m-80) REVERT: A 753 ILE cc_start: 0.6022 (OUTLIER) cc_final: 0.5655 (pt) REVERT: A 1188 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8729 (tp) REVERT: A 1229 ILE cc_start: 0.3263 (OUTLIER) cc_final: 0.2994 (tp) REVERT: A 1394 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: A 1747 CYS cc_start: 0.3033 (OUTLIER) cc_final: 0.2219 (p) REVERT: A 1981 MET cc_start: 0.3449 (OUTLIER) cc_final: 0.2649 (ptt) outliers start: 74 outliers final: 47 residues processed: 133 average time/residue: 0.0719 time to fit residues: 16.1260 Evaluate side-chains 112 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 55 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 255 PRO Chi-restraints excluded: chain A residue 279 SER 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 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 753 ILE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1031 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 1188 LEU Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE 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 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 1394 ASP 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 1460 SER 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 1981 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 63 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 117 optimal weight: 0.0570 chunk 18 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 178 optimal weight: 0.0060 chunk 165 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 overall best weight: 2.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.134908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.120065 restraints weight = 95017.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.118621 restraints weight = 96659.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.119022 restraints weight = 75629.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.119079 restraints weight = 59659.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.119184 restraints weight = 58784.007| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 14098 Z= 0.159 Angle : 0.704 10.549 19455 Z= 0.353 Chirality : 0.044 0.185 2303 Planarity : 0.006 0.083 2537 Dihedral : 5.614 29.217 2013 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.91 % Favored : 91.83 % Rotamer: Outliers : 3.90 % Allowed : 29.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.19), residues: 1884 helix: 0.30 (0.61), residues: 74 sheet: 0.10 (0.27), residues: 376 loop : -1.24 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1712 TYR 0.022 0.002 TYR A 385 PHE 0.017 0.001 PHE A1605 TRP 0.015 0.002 TRP A1397 HIS 0.009 0.002 HIS A1276 Details of bonding type rmsd covalent geometry : bond 0.00366 (14067) covalent geometry : angle 0.70292 (19393) SS BOND : bond 0.00440 ( 31) SS BOND : angle 1.07288 ( 62) hydrogen bonds : bond 0.02873 ( 275) hydrogen bonds : angle 6.15608 ( 672) *********************** 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 114 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 56 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6151 (m-10) REVERT: A 606 TYR cc_start: 0.0034 (OUTLIER) cc_final: -0.0517 (m-10) REVERT: A 662 PHE cc_start: -0.2754 (OUTLIER) cc_final: -0.3064 (m-80) REVERT: A 753 ILE cc_start: 0.5822 (OUTLIER) cc_final: 0.5497 (pt) REVERT: A 1101 MET cc_start: 0.5839 (mmp) cc_final: 0.5492 (mmp) REVERT: A 1229 ILE cc_start: 0.2844 (OUTLIER) cc_final: 0.2499 (tp) REVERT: A 1286 LYS cc_start: 0.8066 (tppp) cc_final: 0.7846 (mmtp) REVERT: A 1480 GLN cc_start: 0.5004 (OUTLIER) cc_final: 0.3008 (tp40) REVERT: A 1747 CYS cc_start: 0.2844 (OUTLIER) cc_final: 0.1981 (p) REVERT: A 1981 MET cc_start: 0.3351 (OUTLIER) cc_final: 0.2773 (ptt) outliers start: 58 outliers final: 42 residues processed: 108 average time/residue: 0.0781 time to fit residues: 13.8999 Evaluate side-chains 106 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 56 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 302 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 606 TYR 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 790 CYS 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 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1031 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 1183 PHE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 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 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 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 1981 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 124 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 169 optimal weight: 40.0000 chunk 105 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.134486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.119617 restraints weight = 94592.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.117789 restraints weight = 94483.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.118149 restraints weight = 78054.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.118273 restraints weight = 64181.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.118400 restraints weight = 56378.379| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14098 Z= 0.164 Angle : 0.691 10.869 19455 Z= 0.346 Chirality : 0.044 0.157 2303 Planarity : 0.006 0.081 2537 Dihedral : 5.390 29.922 2013 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.08 % Favored : 90.61 % Rotamer: Outliers : 3.43 % Allowed : 29.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.19), residues: 1884 helix: 0.39 (0.61), residues: 74 sheet: 0.15 (0.27), residues: 366 loop : -1.21 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1712 TYR 0.019 0.002 TYR A 385 PHE 0.015 0.001 PHE A1538 TRP 0.014 0.002 TRP A1397 HIS 0.011 0.003 HIS A1276 Details of bonding type rmsd covalent geometry : bond 0.00379 (14067) covalent geometry : angle 0.68931 (19393) SS BOND : bond 0.00612 ( 31) SS BOND : angle 1.10341 ( 62) hydrogen bonds : bond 0.02816 ( 275) hydrogen bonds : angle 5.97730 ( 672) ********************** 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 113 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 62 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.6199 (m-10) REVERT: A 606 TYR cc_start: 0.0040 (OUTLIER) cc_final: -0.0465 (m-10) REVERT: A 662 PHE cc_start: -0.2702 (OUTLIER) cc_final: -0.4083 (m-80) REVERT: A 753 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5579 (pt) REVERT: A 1101 MET cc_start: 0.5845 (mmp) cc_final: 0.5524 (mmp) REVERT: A 1229 ILE cc_start: 0.2691 (OUTLIER) cc_final: 0.2324 (tp) REVERT: A 1282 GLU cc_start: 0.6644 (mp0) cc_final: 0.6337 (mp0) REVERT: A 1286 LYS cc_start: 0.8038 (tppp) cc_final: 0.7797 (mmtp) REVERT: A 1480 GLN cc_start: 0.5138 (OUTLIER) cc_final: 0.3063 (tp40) REVERT: A 1497 MET cc_start: 0.7965 (mpp) cc_final: 0.7550 (mmm) REVERT: A 1747 CYS cc_start: 0.3012 (OUTLIER) cc_final: 0.2106 (p) REVERT: A 1981 MET cc_start: 0.3448 (OUTLIER) cc_final: 0.2813 (ptt) outliers start: 51 outliers final: 42 residues processed: 108 average time/residue: 0.0769 time to fit residues: 13.6939 Evaluate side-chains 108 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 58 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 302 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 606 TYR 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 790 CYS 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 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1031 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 1229 ILE 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 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 1418 PHE Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1465 CYS 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 1981 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 71 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 0.3980 chunk 65 optimal weight: 20.0000 chunk 157 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.134884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.120341 restraints weight = 95499.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.118616 restraints weight = 94188.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.119296 restraints weight = 73077.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.119291 restraints weight = 62211.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.119358 restraints weight = 57368.866| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5572 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14098 Z= 0.132 Angle : 0.661 10.887 19455 Z= 0.327 Chirality : 0.043 0.207 2303 Planarity : 0.006 0.088 2537 Dihedral : 5.132 26.535 2013 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.32 % Favored : 92.36 % Rotamer: Outliers : 3.43 % Allowed : 29.70 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.20), residues: 1884 helix: 0.88 (0.64), residues: 68 sheet: 0.14 (0.27), residues: 378 loop : -1.13 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1712 TYR 0.019 0.001 TYR A 385 PHE 0.010 0.001 PHE A1538 TRP 0.012 0.001 TRP A1417 HIS 0.006 0.002 HIS A 847 Details of bonding type rmsd covalent geometry : bond 0.00314 (14067) covalent geometry : angle 0.65976 (19393) SS BOND : bond 0.00358 ( 31) SS BOND : angle 0.88973 ( 62) hydrogen bonds : bond 0.02513 ( 275) hydrogen bonds : angle 5.76131 ( 672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.70 seconds wall clock time: 47 minutes 57.42 seconds (2877.42 seconds total)