Starting phenix.real_space_refine on Thu Jul 31 23:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tx1_41674/07_2025/8tx1_41674.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tx1_41674/07_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_41674/07_2025/8tx1_41674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tx1_41674/07_2025/8tx1_41674.map" model { file = "/net/cci-nas-00/data/ceres_data/8tx1_41674/07_2025/8tx1_41674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tx1_41674/07_2025/8tx1_41674.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 83 5.16 5 C 8643 2.51 5 N 2234 2.21 5 O 2727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13687 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1894, 13687 Classifications: {'peptide': 1894} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 4, 'PTRANS': 195, 'TRANS': 1694} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 9.14, per 1000 atoms: 0.67 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: 3.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 39 sheets defined 4.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 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: 5.89 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.16: 1 1.16 - 1.33: 3260 1.33 - 1.50: 5227 1.50 - 1.67: 5475 1.67 - 1.84: 104 Bond restraints: 14067 Sorted by residual: bond pdb=" CB PRO A 902 " pdb=" CG PRO A 902 " ideal model delta sigma weight residual 1.492 0.991 0.501 5.00e-02 4.00e+02 1.00e+02 bond pdb=" CG PRO A 902 " pdb=" CD PRO A 902 " ideal model delta sigma weight residual 1.503 1.276 0.227 3.40e-02 8.65e+02 4.45e+01 bond pdb=" CG PRO A1528 " pdb=" CD PRO A1528 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.09e+00 bond pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 1.492 1.621 -0.129 5.00e-02 4.00e+02 6.69e+00 bond pdb=" CB PRO A1288 " pdb=" CG PRO A1288 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.65e+00 ... (remaining 14062 not shown) Histogram of bond angle deviations from ideal: 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 35.560 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.960 ------------------------------------------------------------------------------- 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 : 12.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.58 % Favored : 93.21 % Rotamer: Outliers : 0.20 % Allowed : 30.85 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1884 helix: 1.38 (0.63), residues: 68 sheet: 1.65 (0.26), residues: 395 loop : -0.42 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 420 HIS 0.002 0.001 HIS A 847 PHE 0.017 0.001 PHE A1538 TYR 0.021 0.001 TYR A1208 ARG 0.010 0.001 ARG A1242 Details of bonding type rmsd hydrogen bonds : bond 0.11986 ( 275) hydrogen bonds : angle 5.91239 ( 672) SS BOND : bond 0.00375 ( 31) SS BOND : angle 1.40323 ( 62) covalent geometry : bond 0.00639 (14067) covalent geometry : angle 0.92167 (19393) *********************** 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 : 1.389 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: 0.2126 time to fit residues: 25.9400 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 : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 1394 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 0.0000 chunk 76 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 0.0670 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN A1061 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1637 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.141391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.128145 restraints weight = 94300.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.127343 restraints weight = 105264.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.127491 restraints weight = 77494.956| |-----------------------------------------------------------------------------| r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5095 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14098 Z= 0.151 Angle : 0.649 8.889 19455 Z= 0.324 Chirality : 0.043 0.173 2303 Planarity : 0.006 0.081 2537 Dihedral : 4.588 36.663 2016 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.53 % Favored : 93.21 % Rotamer: Outliers : 3.90 % Allowed : 27.28 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1884 helix: 1.22 (0.63), residues: 68 sheet: 1.47 (0.26), residues: 382 loop : -0.48 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 420 HIS 0.003 0.002 HIS A 411 PHE 0.018 0.001 PHE A1538 TYR 0.021 0.001 TYR A1208 ARG 0.008 0.001 ARG A1242 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 275) hydrogen bonds : angle 5.27586 ( 672) SS BOND : bond 0.00470 ( 31) SS BOND : angle 1.19405 ( 62) covalent geometry : bond 0.00356 (14067) covalent geometry : angle 0.64640 (19393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 77 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 833 PHE cc_start: 0.7963 (m-80) cc_final: 0.7618 (m-10) REVERT: A 966 MET cc_start: -0.1317 (mtm) cc_final: -0.1667 (mtm) REVERT: A 1101 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6708 (mmp) REVERT: A 1229 ILE cc_start: 0.2698 (OUTLIER) cc_final: 0.2165 (tp) REVERT: A 1252 ILE cc_start: 0.5353 (OUTLIER) cc_final: 0.4971 (mm) REVERT: A 1269 THR cc_start: 0.2609 (OUTLIER) cc_final: 0.2095 (p) REVERT: A 1421 GLN cc_start: 0.4731 (OUTLIER) cc_final: 0.2825 (mt0) REVERT: A 1480 GLN cc_start: 0.5444 (OUTLIER) cc_final: 0.3686 (tp40) outliers start: 58 outliers final: 29 residues processed: 124 average time/residue: 0.2046 time to fit residues: 42.3214 Evaluate side-chains 103 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1101 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1361 CYS Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1506 ASN Chi-restraints excluded: chain A residue 1588 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 144 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 172 optimal weight: 50.0000 chunk 160 optimal weight: 50.0000 chunk 31 optimal weight: 4.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN A1058 GLN ** A1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.138380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.124042 restraints weight = 95834.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.122390 restraints weight = 99590.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.122859 restraints weight = 76204.131| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 14098 Z= 0.227 Angle : 0.730 9.741 19455 Z= 0.378 Chirality : 0.046 0.204 2303 Planarity : 0.007 0.084 2537 Dihedral : 5.218 30.157 2013 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.07 % Favored : 91.61 % Rotamer: Outliers : 5.58 % Allowed : 26.81 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 1884 helix: 0.80 (0.64), residues: 68 sheet: 0.94 (0.26), residues: 396 loop : -0.77 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1236 HIS 0.006 0.002 HIS A1272 PHE 0.022 0.002 PHE A1538 TYR 0.027 0.002 TYR A1453 ARG 0.010 0.001 ARG A1242 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 275) hydrogen bonds : angle 5.92968 ( 672) SS BOND : bond 0.00647 ( 31) SS BOND : angle 1.49429 ( 62) covalent geometry : bond 0.00497 (14067) covalent geometry : angle 0.72629 (19393) *********************** 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 157 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 74 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASN cc_start: 0.6270 (m-40) cc_final: 0.5941 (t0) REVERT: A 662 PHE cc_start: -0.2174 (OUTLIER) cc_final: -0.2683 (m-80) REVERT: A 966 MET cc_start: -0.1820 (mtm) cc_final: -0.2082 (mtm) REVERT: A 1201 VAL cc_start: 0.3431 (OUTLIER) cc_final: 0.1942 (t) REVERT: A 1229 ILE cc_start: 0.3210 (OUTLIER) cc_final: 0.2926 (tp) REVERT: A 1252 ILE cc_start: 0.6227 (OUTLIER) cc_final: 0.5884 (mm) REVERT: A 1269 THR cc_start: 0.6355 (OUTLIER) cc_final: 0.5898 (t) REVERT: A 1453 TYR cc_start: 0.5505 (OUTLIER) cc_final: 0.4435 (t80) REVERT: A 1747 CYS cc_start: 0.3519 (OUTLIER) cc_final: 0.2784 (p) outliers start: 83 outliers final: 46 residues processed: 144 average time/residue: 0.1888 time to fit residues: 46.0176 Evaluate side-chains 120 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 67 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 205 SER Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 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 599 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 860 THR 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 1024 THR Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1064 SER 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 1131 TYR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1183 PHE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1287 CYS 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 1361 CYS Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1453 TYR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1900 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 141 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 184 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 166 optimal weight: 0.0770 chunk 172 optimal weight: 5.9990 chunk 112 optimal weight: 0.0870 chunk 65 optimal weight: 10.0000 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.139823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.125544 restraints weight = 95426.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.124250 restraints weight = 83115.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.124448 restraints weight = 71363.332| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14098 Z= 0.111 Angle : 0.603 7.499 19455 Z= 0.300 Chirality : 0.042 0.180 2303 Planarity : 0.005 0.074 2537 Dihedral : 4.532 23.638 2013 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.00 % Favored : 93.74 % Rotamer: Outliers : 3.70 % Allowed : 28.29 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1884 helix: 1.20 (0.65), residues: 68 sheet: 1.18 (0.27), residues: 377 loop : -0.69 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 639 HIS 0.003 0.001 HIS A 847 PHE 0.012 0.001 PHE A1538 TYR 0.016 0.001 TYR A1453 ARG 0.006 0.000 ARG A1242 Details of bonding type rmsd hydrogen bonds : bond 0.02397 ( 275) hydrogen bonds : angle 5.26247 ( 672) SS BOND : bond 0.00385 ( 31) SS BOND : angle 0.85187 ( 62) covalent geometry : bond 0.00258 (14067) covalent geometry : angle 0.60187 (19393) *********************** 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 129 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 74 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.2211 (OUTLIER) cc_final: -0.2891 (m-80) REVERT: A 753 ILE cc_start: 0.5860 (OUTLIER) cc_final: 0.5533 (pt) REVERT: A 1421 GLN cc_start: 0.5017 (OUTLIER) cc_final: 0.3349 (tt0) REVERT: A 1436 THR cc_start: 0.7179 (OUTLIER) cc_final: 0.6862 (p) REVERT: A 1480 GLN cc_start: 0.5171 (OUTLIER) cc_final: 0.3258 (tp40) REVERT: A 1747 CYS cc_start: 0.3445 (OUTLIER) cc_final: 0.2529 (p) outliers start: 55 outliers final: 31 residues processed: 115 average time/residue: 0.2042 time to fit residues: 39.5151 Evaluate side-chains 101 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 64 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1183 PHE Chi-restraints excluded: chain A residue 1201 VAL 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 1394 ASP Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 179 optimal weight: 0.0980 chunk 143 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 170 optimal weight: 40.0000 chunk 64 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 119 optimal weight: 0.0050 chunk 60 optimal weight: 0.3980 chunk 138 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.139933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.125693 restraints weight = 94667.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.124358 restraints weight = 84840.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.124558 restraints weight = 74846.286| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14098 Z= 0.102 Angle : 0.579 7.681 19455 Z= 0.285 Chirality : 0.041 0.164 2303 Planarity : 0.005 0.068 2537 Dihedral : 4.220 21.937 2013 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.48 % Favored : 93.26 % Rotamer: Outliers : 3.56 % Allowed : 28.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1884 helix: 1.37 (0.65), residues: 68 sheet: 1.08 (0.27), residues: 383 loop : -0.65 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 312 HIS 0.006 0.001 HIS A 847 PHE 0.034 0.001 PHE A 961 TYR 0.020 0.001 TYR A 385 ARG 0.003 0.000 ARG A1712 Details of bonding type rmsd hydrogen bonds : bond 0.02124 ( 275) hydrogen bonds : angle 4.94910 ( 672) SS BOND : bond 0.00275 ( 31) SS BOND : angle 0.84214 ( 62) covalent geometry : bond 0.00239 (14067) covalent geometry : angle 0.57770 (19393) *********************** 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 123 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 70 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.2288 (OUTLIER) cc_final: -0.2961 (m-80) REVERT: A 753 ILE cc_start: 0.5860 (OUTLIER) cc_final: 0.5581 (pt) REVERT: A 792 MET cc_start: -0.1033 (mtm) cc_final: -0.1895 (mtm) REVERT: A 1421 GLN cc_start: 0.4665 (OUTLIER) cc_final: 0.2929 (tt0) REVERT: A 1480 GLN cc_start: 0.5033 (OUTLIER) cc_final: 0.3167 (tp40) REVERT: A 1747 CYS cc_start: 0.3213 (OUTLIER) cc_final: 0.2406 (p) outliers start: 53 outliers final: 40 residues processed: 113 average time/residue: 0.2648 time to fit residues: 50.7584 Evaluate side-chains 109 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 64 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 223 ILE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 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 599 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 1024 THR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1073 VAL 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 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1361 CYS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 PHE Chi-restraints excluded: chain A residue 1421 GLN Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1480 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 40 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 100 optimal weight: 0.2980 chunk 152 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.138037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.124201 restraints weight = 96110.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.122860 restraints weight = 99375.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.123049 restraints weight = 77386.700| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14098 Z= 0.152 Angle : 0.623 8.018 19455 Z= 0.314 Chirality : 0.042 0.166 2303 Planarity : 0.006 0.068 2537 Dihedral : 4.553 24.712 2013 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.38 % Favored : 92.30 % Rotamer: Outliers : 4.64 % Allowed : 28.09 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1884 helix: 1.14 (0.64), residues: 68 sheet: 1.01 (0.26), residues: 387 loop : -0.79 (0.17), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1236 HIS 0.004 0.002 HIS A1276 PHE 0.027 0.001 PHE A 961 TYR 0.017 0.001 TYR A1291 ARG 0.003 0.000 ARG A1179 Details of bonding type rmsd hydrogen bonds : bond 0.02516 ( 275) hydrogen bonds : angle 5.19239 ( 672) SS BOND : bond 0.00390 ( 31) SS BOND : angle 1.09205 ( 62) covalent geometry : bond 0.00347 (14067) covalent geometry : angle 0.62141 (19393) *********************** 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 137 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 68 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASN cc_start: 0.6166 (OUTLIER) cc_final: 0.5820 (t0) REVERT: A 662 PHE cc_start: -0.2304 (OUTLIER) cc_final: -0.2817 (m-80) REVERT: A 753 ILE cc_start: 0.6023 (OUTLIER) cc_final: 0.5706 (pt) REVERT: A 817 CYS cc_start: 0.2200 (OUTLIER) cc_final: 0.1984 (t) REVERT: A 1229 ILE cc_start: 0.2407 (OUTLIER) cc_final: 0.1925 (tp) REVERT: A 1252 ILE cc_start: 0.6238 (OUTLIER) cc_final: 0.6034 (mm) REVERT: A 1421 GLN cc_start: 0.5525 (OUTLIER) cc_final: 0.3701 (mt0) REVERT: A 1436 THR cc_start: 0.7548 (OUTLIER) cc_final: 0.6949 (p) REVERT: A 1480 GLN cc_start: 0.5236 (OUTLIER) cc_final: 0.3117 (tp40) REVERT: A 1747 CYS cc_start: 0.3181 (OUTLIER) cc_final: 0.2388 (p) outliers start: 69 outliers final: 44 residues processed: 127 average time/residue: 0.1910 time to fit residues: 40.2096 Evaluate side-chains 118 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 64 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 229 ASN Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 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 599 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 817 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 1024 THR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 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 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 171 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1049 GLN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.136703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.121051 restraints weight = 95416.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.119843 restraints weight = 73091.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.120154 restraints weight = 61442.875| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14098 Z= 0.170 Angle : 0.665 10.082 19455 Z= 0.336 Chirality : 0.043 0.181 2303 Planarity : 0.006 0.073 2537 Dihedral : 5.002 25.766 2013 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.96 % Favored : 91.72 % Rotamer: Outliers : 4.10 % Allowed : 28.97 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1884 helix: 0.86 (0.63), residues: 68 sheet: 0.72 (0.26), residues: 386 loop : -0.96 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1397 HIS 0.006 0.002 HIS A1276 PHE 0.019 0.002 PHE A 961 TYR 0.020 0.002 TYR A1291 ARG 0.003 0.001 ARG A1227 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 275) hydrogen bonds : angle 5.54309 ( 672) SS BOND : bond 0.00426 ( 31) SS BOND : angle 1.11353 ( 62) covalent geometry : bond 0.00386 (14067) covalent geometry : angle 0.66321 (19393) *********************** 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 125 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 64 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.2164 (OUTLIER) cc_final: -0.2651 (m-80) REVERT: A 753 ILE cc_start: 0.6148 (OUTLIER) cc_final: 0.5917 (pt) REVERT: A 1229 ILE cc_start: 0.2759 (OUTLIER) cc_final: 0.2357 (tp) REVERT: A 1480 GLN cc_start: 0.5074 (OUTLIER) cc_final: 0.2882 (tp40) REVERT: A 1747 CYS cc_start: 0.3327 (OUTLIER) cc_final: 0.2564 (p) REVERT: A 1981 MET cc_start: 0.3399 (OUTLIER) cc_final: 0.3058 (ptt) outliers start: 61 outliers final: 44 residues processed: 118 average time/residue: 0.2890 time to fit residues: 58.6621 Evaluate side-chains 114 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 64 time to evaluate : 1.951 ------------------------------------------------------------------------------- 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 223 ILE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL 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 1172 VAL Chi-restraints excluded: chain A residue 1183 PHE Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 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 1421 GLN Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 121 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.0050 chunk 152 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 130 optimal weight: 0.0170 chunk 175 optimal weight: 30.0000 chunk 120 optimal weight: 4.9990 overall best weight: 2.0038 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.136899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.122682 restraints weight = 95464.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.121108 restraints weight = 93687.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.121493 restraints weight = 80926.420| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5478 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14098 Z= 0.137 Angle : 0.631 10.922 19455 Z= 0.314 Chirality : 0.042 0.165 2303 Planarity : 0.006 0.077 2537 Dihedral : 4.811 25.299 2013 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.06 % Favored : 92.62 % Rotamer: Outliers : 3.83 % Allowed : 28.76 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1884 helix: 1.00 (0.64), residues: 68 sheet: 0.68 (0.26), residues: 386 loop : -0.95 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1397 HIS 0.004 0.001 HIS A 847 PHE 0.012 0.001 PHE A1418 TYR 0.016 0.001 TYR A1029 ARG 0.003 0.000 ARG A1712 Details of bonding type rmsd hydrogen bonds : bond 0.02636 ( 275) hydrogen bonds : angle 5.44295 ( 672) SS BOND : bond 0.00616 ( 31) SS BOND : angle 0.94028 ( 62) covalent geometry : bond 0.00317 (14067) covalent geometry : angle 0.62938 (19393) *********************** 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 122 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 65 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 662 PHE cc_start: -0.2556 (OUTLIER) cc_final: -0.3015 (m-80) REVERT: A 753 ILE cc_start: 0.6003 (OUTLIER) cc_final: 0.5697 (pt) REVERT: A 1229 ILE cc_start: 0.1857 (OUTLIER) cc_final: 0.1458 (tp) REVERT: A 1421 GLN cc_start: 0.4806 (OUTLIER) cc_final: 0.3804 (tt0) REVERT: A 1480 GLN cc_start: 0.4900 (OUTLIER) cc_final: 0.2663 (tp40) REVERT: A 1747 CYS cc_start: 0.3183 (OUTLIER) cc_final: 0.2295 (p) REVERT: A 1981 MET cc_start: 0.2947 (OUTLIER) cc_final: 0.2620 (ptt) outliers start: 57 outliers final: 44 residues processed: 116 average time/residue: 0.2455 time to fit residues: 49.0011 Evaluate side-chains 110 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 59 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 223 ILE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 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 599 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL 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 1172 VAL Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1317 CYS Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1361 CYS Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 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 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 1747 CYS Chi-restraints excluded: chain A residue 1871 ARG Chi-restraints excluded: chain A residue 1981 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 20 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 164 optimal weight: 40.0000 chunk 123 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4640 r_free = 0.4640 target = 0.136621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.120744 restraints weight = 94920.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.119858 restraints weight = 69848.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.120256 restraints weight = 62013.486| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5613 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14098 Z= 0.132 Angle : 0.627 11.461 19455 Z= 0.311 Chirality : 0.042 0.160 2303 Planarity : 0.006 0.074 2537 Dihedral : 4.660 24.689 2013 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.38 % Favored : 92.30 % Rotamer: Outliers : 4.03 % Allowed : 28.63 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1884 helix: 1.06 (0.64), residues: 68 sheet: 0.65 (0.26), residues: 388 loop : -0.94 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1397 HIS 0.004 0.001 HIS A 847 PHE 0.011 0.001 PHE A1538 TYR 0.015 0.001 TYR A1131 ARG 0.003 0.000 ARG A1712 Details of bonding type rmsd hydrogen bonds : bond 0.02512 ( 275) hydrogen bonds : angle 5.31782 ( 672) SS BOND : bond 0.00326 ( 31) SS BOND : angle 0.93064 ( 62) covalent geometry : bond 0.00307 (14067) covalent geometry : angle 0.62585 (19393) *********************** 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 122 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 62 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.6050 (m-80) REVERT: A 306 LEU cc_start: 0.4488 (OUTLIER) cc_final: 0.4057 (mt) REVERT: A 662 PHE cc_start: -0.2566 (OUTLIER) cc_final: -0.3009 (m-80) REVERT: A 753 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5818 (pt) REVERT: A 1229 ILE cc_start: 0.2704 (OUTLIER) cc_final: 0.2239 (tp) REVERT: A 1286 LYS cc_start: 0.7703 (mmmt) cc_final: 0.7128 (tptt) REVERT: A 1421 GLN cc_start: 0.4347 (OUTLIER) cc_final: 0.3377 (tt0) REVERT: A 1480 GLN cc_start: 0.5021 (OUTLIER) cc_final: 0.2776 (tp40) REVERT: A 1747 CYS cc_start: 0.3297 (OUTLIER) cc_final: 0.2437 (p) REVERT: A 1981 MET cc_start: 0.3035 (OUTLIER) cc_final: 0.2537 (ptt) outliers start: 60 outliers final: 48 residues processed: 116 average time/residue: 0.1990 time to fit residues: 37.9325 Evaluate side-chains 116 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 59 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 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 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL 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 1172 VAL Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 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 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 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 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 178 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 150 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- 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 = 0.4649 r_free = 0.4649 target = 0.137234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.122828 restraints weight = 95693.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.121636 restraints weight = 96514.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.121736 restraints weight = 82298.790| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5454 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14098 Z= 0.110 Angle : 0.620 16.668 19455 Z= 0.299 Chirality : 0.042 0.182 2303 Planarity : 0.005 0.074 2537 Dihedral : 4.435 22.315 2013 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.21 % Favored : 93.47 % Rotamer: Outliers : 3.76 % Allowed : 28.90 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1884 helix: 1.22 (0.65), residues: 68 sheet: 0.69 (0.26), residues: 384 loop : -0.87 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 190 HIS 0.004 0.001 HIS A 847 PHE 0.011 0.001 PHE A 961 TYR 0.018 0.001 TYR A1029 ARG 0.002 0.000 ARG A1712 Details of bonding type rmsd hydrogen bonds : bond 0.02277 ( 275) hydrogen bonds : angle 5.11152 ( 672) SS BOND : bond 0.00272 ( 31) SS BOND : angle 0.78092 ( 62) covalent geometry : bond 0.00261 (14067) covalent geometry : angle 0.61928 (19393) ********************** 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 120 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 64 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 LEU cc_start: 0.4647 (OUTLIER) cc_final: 0.4194 (mt) REVERT: A 662 PHE cc_start: -0.2743 (OUTLIER) cc_final: -0.3183 (m-80) REVERT: A 753 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5592 (pt) REVERT: A 1229 ILE cc_start: 0.2396 (OUTLIER) cc_final: 0.1938 (tp) REVERT: A 1286 LYS cc_start: 0.7399 (mmmt) cc_final: 0.6953 (tppt) REVERT: A 1421 GLN cc_start: 0.4259 (OUTLIER) cc_final: 0.2980 (tt0) REVERT: A 1480 GLN cc_start: 0.5087 (OUTLIER) cc_final: 0.2792 (tp40) REVERT: A 1747 CYS cc_start: 0.3146 (OUTLIER) cc_final: 0.2233 (p) REVERT: A 1981 MET cc_start: 0.2689 (OUTLIER) cc_final: 0.2230 (ptt) outliers start: 56 outliers final: 44 residues processed: 113 average time/residue: 0.3294 time to fit residues: 63.0175 Evaluate side-chains 112 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 60 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 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 536 PHE Chi-restraints excluded: chain A residue 594 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1196 THR 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 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 1421 GLN Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1432 VAL Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 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 53 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 171 optimal weight: 0.5980 chunk 69 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 125 optimal weight: 0.0030 chunk 73 optimal weight: 5.9990 overall best weight: 2.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.136254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.123051 restraints weight = 96098.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.121986 restraints weight = 91944.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.122478 restraints weight = 71899.552| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5370 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14098 Z= 0.142 Angle : 0.648 16.411 19455 Z= 0.317 Chirality : 0.043 0.179 2303 Planarity : 0.006 0.073 2537 Dihedral : 4.604 25.088 2013 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.86 % Favored : 91.83 % Rotamer: Outliers : 3.90 % Allowed : 28.70 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1884 helix: 1.08 (0.64), residues: 68 sheet: 0.69 (0.26), residues: 386 loop : -0.94 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1397 HIS 0.003 0.001 HIS A 847 PHE 0.012 0.001 PHE A1538 TYR 0.019 0.001 TYR A1029 ARG 0.007 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.02499 ( 275) hydrogen bonds : angle 5.23718 ( 672) SS BOND : bond 0.00408 ( 31) SS BOND : angle 0.94230 ( 62) covalent geometry : bond 0.00330 (14067) covalent geometry : angle 0.64691 (19393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6216.67 seconds wall clock time: 114 minutes 9.37 seconds (6849.37 seconds total)