Starting phenix.real_space_refine on Wed Mar 4 01:37:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fbs_31519/03_2026/7fbs_31519.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fbs_31519/03_2026/7fbs_31519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fbs_31519/03_2026/7fbs_31519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fbs_31519/03_2026/7fbs_31519.map" model { file = "/net/cci-nas-00/data/ceres_data/7fbs_31519/03_2026/7fbs_31519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fbs_31519/03_2026/7fbs_31519.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.096 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 65 5.16 5 C 6196 2.51 5 N 1414 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8849 Classifications: {'peptide': 1118} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 30, 'TRANS': 1087} Chain breaks: 6 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 425 Unusual residues: {'4Y4': 1, '6OU': 11, '9Z9': 2, 'NAG': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'6OU:plan-1': 8, '6OU:plan-3': 1, '6OU:plan-2': 2} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 2.17, per 1000 atoms: 0.23 Number of scatterers: 9274 At special positions: 0 Unit cell: (127.776, 127.776, 107.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 5 15.00 O 1594 8.00 N 1414 7.00 C 6196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.02 Simple disulfide: pdb=" SG CYS A1365 " - pdb=" SG CYS A1386 " distance=2.03 Simple disulfide: pdb=" SG CYS A1730 " - pdb=" SG CYS A1744 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 431.4 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 1 sheets defined 78.3% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 119 through 131 Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.154A pdb=" N SER A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 158 through 181 removed outlier: 3.567A pdb=" N ALA A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 192 removed outlier: 4.017A pdb=" N ASP A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 211 removed outlier: 4.179A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.601A pdb=" N THR A 221 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 223 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.951A pdb=" N LEU A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.577A pdb=" N LYS A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 251 removed outlier: 3.619A pdb=" N LYS A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 274 Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.856A pdb=" N LEU A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 401 through 429 Processing helix chain 'A' and resid 705 through 715 Processing helix chain 'A' and resid 720 through 736 Processing helix chain 'A' and resid 743 through 772 removed outlier: 4.010A pdb=" N LEU A 772 " --> pdb=" O LYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 780 Processing helix chain 'A' and resid 780 through 797 Processing helix chain 'A' and resid 806 through 822 removed outlier: 3.715A pdb=" N ARG A 809 " --> pdb=" O SER A 806 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 812 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 814 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 821 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 837 removed outlier: 3.733A pdb=" N VAL A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 869 removed outlier: 5.539A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASN A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 873 Processing helix chain 'A' and resid 886 through 900 Processing helix chain 'A' and resid 902 through 913 removed outlier: 3.820A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 944 Processing helix chain 'A' and resid 1191 through 1206 Processing helix chain 'A' and resid 1206 through 1225 Processing helix chain 'A' and resid 1234 through 1264 removed outlier: 3.609A pdb=" N VAL A1239 " --> pdb=" O LYS A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1270 Processing helix chain 'A' and resid 1271 through 1293 Processing helix chain 'A' and resid 1299 through 1305 removed outlier: 3.819A pdb=" N ARG A1305 " --> pdb=" O ILE A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1313 Proline residue: A1312 - end of helix Processing helix chain 'A' and resid 1314 through 1319 removed outlier: 4.233A pdb=" N ARG A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A1319 " --> pdb=" O ALA A1315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1319' Processing helix chain 'A' and resid 1321 through 1331 Processing helix chain 'A' and resid 1332 through 1358 removed outlier: 3.561A pdb=" N ILE A1336 " --> pdb=" O ALA A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1389 Processing helix chain 'A' and resid 1406 through 1419 Processing helix chain 'A' and resid 1422 through 1431 removed outlier: 3.752A pdb=" N ILE A1426 " --> pdb=" O GLY A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1447 No H-bonds generated for 'chain 'A' and resid 1445 through 1447' Processing helix chain 'A' and resid 1448 through 1459 removed outlier: 3.662A pdb=" N PHE A1452 " --> pdb=" O MET A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1481 Processing helix chain 'A' and resid 1491 through 1503 Processing helix chain 'A' and resid 1517 through 1529 removed outlier: 3.736A pdb=" N LYS A1529 " --> pdb=" O ASP A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1549 removed outlier: 3.687A pdb=" N ASP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1582 removed outlier: 3.747A pdb=" N ALA A1582 " --> pdb=" O ILE A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1591 removed outlier: 3.657A pdb=" N THR A1590 " --> pdb=" O HIS A1586 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A1591 " --> pdb=" O TYR A1587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1586 through 1591' Processing helix chain 'A' and resid 1591 through 1613 Processing helix chain 'A' and resid 1622 through 1628 removed outlier: 3.882A pdb=" N VAL A1626 " --> pdb=" O THR A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1637 removed outlier: 4.132A pdb=" N ILE A1635 " --> pdb=" O ARG A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1641 Processing helix chain 'A' and resid 1643 through 1655 removed outlier: 3.683A pdb=" N SER A1655 " --> pdb=" O ALA A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1681 Processing helix chain 'A' and resid 1698 through 1711 removed outlier: 3.655A pdb=" N SER A1702 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1724 Proline residue: A1721 - end of helix removed outlier: 3.732A pdb=" N ASN A1724 " --> pdb=" O SER A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1777 Processing sheet with id=AA1, first strand: chain 'A' and resid 1366 through 1367 600 hydrogen bonds defined for protein. 1749 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: 1.58 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.49: 5389 1.49 - 1.83: 4097 1.83 - 2.18: 0 2.18 - 2.53: 0 2.53 - 2.88: 1 Bond restraints: 9487 Sorted by residual: bond pdb=" C22 9Z9 A2216 " pdb=" C23 9Z9 A2216 " ideal model delta sigma weight residual 1.534 2.876 -1.342 2.00e-02 2.50e+03 4.50e+03 bond pdb=" C06 9Z9 A2216 " pdb=" C07 9Z9 A2216 " ideal model delta sigma weight residual 1.520 1.141 0.379 2.00e-02 2.50e+03 3.59e+02 bond pdb=" C06 9Z9 A2217 " pdb=" C07 9Z9 A2217 " ideal model delta sigma weight residual 1.520 1.146 0.374 2.00e-02 2.50e+03 3.50e+02 bond pdb=" C11 9Z9 A2217 " pdb=" C13 9Z9 A2217 " ideal model delta sigma weight residual 1.519 1.160 0.359 2.00e-02 2.50e+03 3.23e+02 bond pdb=" C11 9Z9 A2216 " pdb=" C13 9Z9 A2216 " ideal model delta sigma weight residual 1.519 1.160 0.359 2.00e-02 2.50e+03 3.22e+02 ... (remaining 9482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 12474 3.28 - 6.57: 290 6.57 - 9.85: 61 9.85 - 13.13: 6 13.13 - 16.41: 5 Bond angle restraints: 12836 Sorted by residual: angle pdb=" C LEU A1373 " pdb=" N PRO A1374 " pdb=" CA PRO A1374 " ideal model delta sigma weight residual 119.84 128.53 -8.69 1.25e+00 6.40e-01 4.84e+01 angle pdb=" N GLN A1368 " pdb=" CA GLN A1368 " pdb=" C GLN A1368 " ideal model delta sigma weight residual 111.28 117.38 -6.10 1.09e+00 8.42e-01 3.13e+01 angle pdb=" O22 6OU A2204 " pdb=" P23 6OU A2204 " pdb=" O26 6OU A2204 " ideal model delta sigma weight residual 93.95 110.36 -16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" O22 6OU A2205 " pdb=" P23 6OU A2205 " pdb=" O26 6OU A2205 " ideal model delta sigma weight residual 93.95 110.23 -16.28 3.00e+00 1.11e-01 2.94e+01 angle pdb=" O22 6OU A2215 " pdb=" P23 6OU A2215 " pdb=" O26 6OU A2215 " ideal model delta sigma weight residual 93.95 109.71 -15.76 3.00e+00 1.11e-01 2.76e+01 ... (remaining 12831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.67: 5408 31.67 - 63.33: 314 63.33 - 95.00: 40 95.00 - 126.67: 16 126.67 - 158.33: 5 Dihedral angle restraints: 5783 sinusoidal: 2522 harmonic: 3261 Sorted by residual: dihedral pdb=" CB CYS A1730 " pdb=" SG CYS A1730 " pdb=" SG CYS A1744 " pdb=" CB CYS A1744 " ideal model delta sinusoidal sigma weight residual 93.00 -179.59 -87.41 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 918 " pdb=" CB CYS A 918 " ideal model delta sinusoidal sigma weight residual 93.00 152.68 -59.68 1 1.00e+01 1.00e-02 4.75e+01 dihedral pdb=" CA ALA A1583 " pdb=" C ALA A1583 " pdb=" N LEU A1584 " pdb=" CA LEU A1584 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 5780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.303: 1477 0.303 - 0.606: 5 0.606 - 0.909: 0 0.909 - 1.212: 2 1.212 - 1.515: 2 Chirality restraints: 1486 Sorted by residual: chirality pdb=" C07 9Z9 A2216 " pdb=" C06 9Z9 A2216 " pdb=" C08 9Z9 A2216 " pdb=" C15 9Z9 A2216 " both_signs ideal model delta sigma weight residual False -2.70 -1.18 -1.52 2.00e-01 2.50e+01 5.74e+01 chirality pdb=" C07 9Z9 A2217 " pdb=" C06 9Z9 A2217 " pdb=" C08 9Z9 A2217 " pdb=" C15 9Z9 A2217 " both_signs ideal model delta sigma weight residual False -2.70 -1.22 -1.48 2.00e-01 2.50e+01 5.46e+01 chirality pdb=" C02 9Z9 A2216 " pdb=" C03 9Z9 A2216 " pdb=" C06 9Z9 A2216 " pdb=" C10 9Z9 A2216 " both_signs ideal model delta sigma weight residual False 2.92 1.97 0.95 2.00e-01 2.50e+01 2.28e+01 ... (remaining 1483 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 348 " -0.044 5.00e-02 4.00e+02 6.54e-02 6.83e+00 pdb=" N PRO A 349 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 349 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 349 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 311 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 312 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 311 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.79e+00 pdb=" C ASP A 311 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP A 311 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO A 312 " -0.013 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 87 2.61 - 3.18: 8819 3.18 - 3.76: 14300 3.76 - 4.33: 19943 4.33 - 4.90: 32169 Nonbonded interactions: 75318 Sorted by model distance: nonbonded pdb=" O MET A1670 " pdb=" OG SER A1674 " model vdw 2.040 3.040 nonbonded pdb=" O GLY A1459 " pdb=" OG1 THR A1463 " model vdw 2.098 3.040 nonbonded pdb=" O LEU A 931 " pdb=" ND2 ASN A 935 " model vdw 2.112 3.120 nonbonded pdb=" O4 NAG A2201 " pdb=" O7 NAG A2202 " model vdw 2.133 3.040 nonbonded pdb=" ND2 ASN A1390 " pdb=" O7 NAG A2201 " model vdw 2.152 3.120 ... (remaining 75313 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.022 1.342 9491 Z= 1.062 Angle : 1.200 16.414 12844 Z= 0.548 Chirality : 0.086 1.515 1486 Planarity : 0.005 0.065 1532 Dihedral : 20.656 158.331 3661 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.43 % Favored : 92.48 % Rotamer: Outliers : 3.06 % Allowed : 21.33 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.22), residues: 1104 helix: -1.88 (0.15), residues: 782 sheet: -5.17 (0.99), residues: 12 loop : -2.72 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 815 TYR 0.018 0.003 TYR A1447 PHE 0.020 0.002 PHE A1452 TRP 0.011 0.002 TRP A 882 HIS 0.006 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.02156 ( 9487) covalent geometry : angle 1.19894 (12836) SS BOND : bond 0.00341 ( 4) SS BOND : angle 1.90336 ( 8) hydrogen bonds : bond 0.13170 ( 600) hydrogen bonds : angle 6.89160 ( 1749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8076 (tmtt) REVERT: A 370 MET cc_start: 0.8126 (tmm) cc_final: 0.7898 (ttt) REVERT: A 705 MET cc_start: 0.4942 (mmp) cc_final: 0.3749 (tmm) REVERT: A 764 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5442 (tm-30) REVERT: A 842 ASN cc_start: 0.7476 (p0) cc_final: 0.7153 (m-40) REVERT: A 1287 SER cc_start: 0.7562 (t) cc_final: 0.7322 (p) REVERT: A 1364 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7400 (mmt90) REVERT: A 1594 ASN cc_start: 0.8025 (m110) cc_final: 0.7703 (m-40) REVERT: A 1603 LEU cc_start: 0.8688 (mt) cc_final: 0.8451 (mt) REVERT: A 1769 TYR cc_start: 0.7959 (m-10) cc_final: 0.7245 (m-10) outliers start: 29 outliers final: 15 residues processed: 237 average time/residue: 0.0943 time to fit residues: 31.3979 Evaluate side-chains 186 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1364 ARG Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1611 SER Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1730 CYS Chi-restraints excluded: chain A residue 1774 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 151 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A 860 GLN A 871 HIS A1327 ASN A1356 ASN ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 ASN A1560 ASN A1701 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.172052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138317 restraints weight = 12152.318| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.75 r_work: 0.3152 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9491 Z= 0.167 Angle : 0.652 12.551 12844 Z= 0.328 Chirality : 0.040 0.162 1486 Planarity : 0.004 0.062 1532 Dihedral : 17.404 142.303 1732 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.91 % Allowed : 21.22 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.24), residues: 1104 helix: -0.35 (0.17), residues: 791 sheet: -4.75 (1.15), residues: 12 loop : -2.01 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1318 TYR 0.015 0.002 TYR A1411 PHE 0.015 0.001 PHE A1598 TRP 0.010 0.001 TRP A 823 HIS 0.003 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9487) covalent geometry : angle 0.65132 (12836) SS BOND : bond 0.00764 ( 4) SS BOND : angle 1.55870 ( 8) hydrogen bonds : bond 0.04241 ( 600) hydrogen bonds : angle 4.89803 ( 1749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.6937 (mtp-110) REVERT: A 370 MET cc_start: 0.8638 (tmm) cc_final: 0.8338 (ttt) REVERT: A 705 MET cc_start: 0.5201 (mmp) cc_final: 0.3744 (tmm) REVERT: A 749 MET cc_start: 0.8696 (tmm) cc_final: 0.8393 (tmm) REVERT: A 842 ASN cc_start: 0.7607 (p0) cc_final: 0.7140 (m-40) REVERT: A 901 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 940 LEU cc_start: 0.9143 (mt) cc_final: 0.8897 (mp) REVERT: A 1302 LYS cc_start: 0.8344 (pttm) cc_final: 0.8115 (pttm) outliers start: 37 outliers final: 16 residues processed: 220 average time/residue: 0.0932 time to fit residues: 29.0288 Evaluate side-chains 173 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1530 GLN Chi-restraints excluded: chain A residue 1645 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 85 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1594 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.172898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139136 restraints weight = 12167.889| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.70 r_work: 0.3180 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9491 Z= 0.142 Angle : 0.611 12.587 12844 Z= 0.308 Chirality : 0.038 0.143 1486 Planarity : 0.004 0.058 1532 Dihedral : 15.389 134.092 1711 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.12 % Allowed : 21.01 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1104 helix: 0.43 (0.18), residues: 788 sheet: -4.49 (1.13), residues: 12 loop : -1.85 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1318 TYR 0.012 0.001 TYR A1447 PHE 0.012 0.001 PHE A1404 TRP 0.011 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9487) covalent geometry : angle 0.61010 (12836) SS BOND : bond 0.00369 ( 4) SS BOND : angle 1.43001 ( 8) hydrogen bonds : bond 0.03892 ( 600) hydrogen bonds : angle 4.55459 ( 1749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7001 (tp30) REVERT: A 223 ARG cc_start: 0.7325 (ptm-80) cc_final: 0.6858 (mtp-110) REVERT: A 327 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8062 (m) REVERT: A 370 MET cc_start: 0.8616 (tmm) cc_final: 0.8327 (ttt) REVERT: A 705 MET cc_start: 0.5450 (mmp) cc_final: 0.3655 (tmm) REVERT: A 749 MET cc_start: 0.8616 (tmm) cc_final: 0.8379 (tmm) REVERT: A 772 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7206 (pt) REVERT: A 777 TYR cc_start: 0.4519 (OUTLIER) cc_final: 0.3800 (m-80) REVERT: A 842 ASN cc_start: 0.7547 (p0) cc_final: 0.7063 (m-40) REVERT: A 901 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 940 LEU cc_start: 0.9140 (mt) cc_final: 0.8894 (mp) REVERT: A 1198 LYS cc_start: 0.6743 (mmpt) cc_final: 0.6428 (ptpt) REVERT: A 1212 PHE cc_start: 0.7352 (t80) cc_final: 0.6985 (t80) REVERT: A 1298 MET cc_start: 0.5930 (ppp) cc_final: 0.5623 (ppp) REVERT: A 1322 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7191 (mpp) REVERT: A 1467 PHE cc_start: 0.7387 (m-80) cc_final: 0.7148 (m-80) REVERT: A 1610 LEU cc_start: 0.8579 (mt) cc_final: 0.8029 (tt) REVERT: A 1653 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7992 (ttp) REVERT: A 1767 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8260 (m-40) REVERT: A 1768 MET cc_start: 0.8550 (mmm) cc_final: 0.8191 (mmm) outliers start: 39 outliers final: 17 residues processed: 208 average time/residue: 0.0830 time to fit residues: 25.3004 Evaluate side-chains 182 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1530 GLN Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1595 ILE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1653 MET Chi-restraints excluded: chain A residue 1730 CYS Chi-restraints excluded: chain A residue 1767 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 79 optimal weight: 0.0870 chunk 19 optimal weight: 0.0270 chunk 106 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A1439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.174671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140516 restraints weight = 12197.557| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.67 r_work: 0.3197 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9491 Z= 0.123 Angle : 0.596 12.721 12844 Z= 0.299 Chirality : 0.038 0.144 1486 Planarity : 0.004 0.058 1532 Dihedral : 14.518 131.683 1709 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.59 % Allowed : 23.13 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.26), residues: 1104 helix: 0.76 (0.18), residues: 793 sheet: -4.53 (1.07), residues: 12 loop : -1.87 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1628 TYR 0.012 0.001 TYR A1411 PHE 0.011 0.001 PHE A1753 TRP 0.027 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9487) covalent geometry : angle 0.59513 (12836) SS BOND : bond 0.00195 ( 4) SS BOND : angle 1.33655 ( 8) hydrogen bonds : bond 0.03681 ( 600) hydrogen bonds : angle 4.40381 ( 1749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7005 (tp30) REVERT: A 223 ARG cc_start: 0.7299 (ptm-80) cc_final: 0.6842 (mtp-110) REVERT: A 370 MET cc_start: 0.8615 (tmm) cc_final: 0.8328 (ttt) REVERT: A 705 MET cc_start: 0.5854 (mmp) cc_final: 0.3811 (tmm) REVERT: A 749 MET cc_start: 0.8598 (tmm) cc_final: 0.8382 (tmm) REVERT: A 772 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7144 (pt) REVERT: A 777 TYR cc_start: 0.4318 (OUTLIER) cc_final: 0.3134 (m-80) REVERT: A 842 ASN cc_start: 0.7426 (p0) cc_final: 0.7007 (m-40) REVERT: A 901 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 940 LEU cc_start: 0.9111 (mt) cc_final: 0.8880 (mp) REVERT: A 1212 PHE cc_start: 0.7338 (t80) cc_final: 0.6960 (t80) REVERT: A 1298 MET cc_start: 0.5849 (ppp) cc_final: 0.5583 (ppp) REVERT: A 1302 LYS cc_start: 0.8334 (pttm) cc_final: 0.8124 (pttm) REVERT: A 1320 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8062 (tm-30) REVERT: A 1322 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7013 (mpp) REVERT: A 1467 PHE cc_start: 0.7362 (m-80) cc_final: 0.7101 (m-80) REVERT: A 1653 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7825 (ttp) REVERT: A 1659 LEU cc_start: 0.8671 (mp) cc_final: 0.8438 (mp) REVERT: A 1767 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8252 (m-40) outliers start: 34 outliers final: 17 residues processed: 205 average time/residue: 0.0779 time to fit residues: 23.7087 Evaluate side-chains 187 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1653 MET Chi-restraints excluded: chain A residue 1730 CYS Chi-restraints excluded: chain A residue 1767 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A1736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.173151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136491 restraints weight = 12206.811| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.86 r_work: 0.3150 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9491 Z= 0.146 Angle : 0.607 10.301 12844 Z= 0.305 Chirality : 0.039 0.127 1486 Planarity : 0.004 0.057 1532 Dihedral : 14.207 126.483 1707 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.65 % Allowed : 22.49 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1104 helix: 0.86 (0.18), residues: 793 sheet: -4.57 (1.03), residues: 12 loop : -1.85 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1628 TYR 0.015 0.001 TYR A 417 PHE 0.012 0.001 PHE A1404 TRP 0.018 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9487) covalent geometry : angle 0.60647 (12836) SS BOND : bond 0.00198 ( 4) SS BOND : angle 1.28138 ( 8) hydrogen bonds : bond 0.03703 ( 600) hydrogen bonds : angle 4.43307 ( 1749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7116 (tp30) REVERT: A 223 ARG cc_start: 0.7464 (ptm-80) cc_final: 0.7016 (mtp-110) REVERT: A 370 MET cc_start: 0.8664 (tmm) cc_final: 0.8378 (ttt) REVERT: A 705 MET cc_start: 0.6012 (mmp) cc_final: 0.3906 (tmm) REVERT: A 749 MET cc_start: 0.8674 (tmm) cc_final: 0.8390 (tmm) REVERT: A 772 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7222 (pt) REVERT: A 777 TYR cc_start: 0.4503 (OUTLIER) cc_final: 0.3251 (m-80) REVERT: A 842 ASN cc_start: 0.7471 (p0) cc_final: 0.7037 (m-40) REVERT: A 901 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 1212 PHE cc_start: 0.7448 (t80) cc_final: 0.7150 (t80) REVERT: A 1298 MET cc_start: 0.5550 (ppp) cc_final: 0.5302 (ppp) REVERT: A 1322 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7035 (mpp) REVERT: A 1445 ASN cc_start: 0.8712 (t0) cc_final: 0.8398 (t0) REVERT: A 1467 PHE cc_start: 0.7606 (m-80) cc_final: 0.7378 (m-80) REVERT: A 1653 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7776 (ttp) REVERT: A 1659 LEU cc_start: 0.8722 (mp) cc_final: 0.8445 (mp) REVERT: A 1767 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8254 (m-40) REVERT: A 1768 MET cc_start: 0.8639 (mmm) cc_final: 0.8289 (mmm) outliers start: 44 outliers final: 27 residues processed: 207 average time/residue: 0.0805 time to fit residues: 24.4523 Evaluate side-chains 201 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1530 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1595 ILE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1653 MET Chi-restraints excluded: chain A residue 1730 CYS Chi-restraints excluded: chain A residue 1767 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 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 = 0.4010 r_free = 0.4010 target = 0.173968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141362 restraints weight = 12185.365| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.65 r_work: 0.3220 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9491 Z= 0.130 Angle : 0.601 12.941 12844 Z= 0.300 Chirality : 0.038 0.160 1486 Planarity : 0.004 0.058 1532 Dihedral : 13.670 124.349 1707 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.33 % Allowed : 23.44 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1104 helix: 0.91 (0.18), residues: 799 sheet: -4.47 (1.06), residues: 12 loop : -1.78 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1628 TYR 0.017 0.001 TYR A1201 PHE 0.010 0.001 PHE A1753 TRP 0.020 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9487) covalent geometry : angle 0.60029 (12836) SS BOND : bond 0.00193 ( 4) SS BOND : angle 1.27440 ( 8) hydrogen bonds : bond 0.03568 ( 600) hydrogen bonds : angle 4.32107 ( 1749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7056 (tp30) REVERT: A 223 ARG cc_start: 0.7306 (ptm-80) cc_final: 0.6875 (mtp-110) REVERT: A 255 MET cc_start: 0.8134 (mmm) cc_final: 0.7697 (mtm) REVERT: A 370 MET cc_start: 0.8578 (tmm) cc_final: 0.8281 (ttt) REVERT: A 705 MET cc_start: 0.6305 (mmp) cc_final: 0.4148 (tmm) REVERT: A 749 MET cc_start: 0.8586 (tmm) cc_final: 0.8365 (tmm) REVERT: A 769 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6690 (tt) REVERT: A 777 TYR cc_start: 0.4455 (OUTLIER) cc_final: 0.3319 (m-80) REVERT: A 842 ASN cc_start: 0.7405 (p0) cc_final: 0.6988 (m-40) REVERT: A 901 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7328 (mt-10) REVERT: A 1198 LYS cc_start: 0.6644 (mmpt) cc_final: 0.6421 (ptpt) REVERT: A 1212 PHE cc_start: 0.7415 (t80) cc_final: 0.7137 (t80) REVERT: A 1238 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7042 (tttt) REVERT: A 1298 MET cc_start: 0.5638 (ppp) cc_final: 0.5255 (ppp) REVERT: A 1322 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6858 (mpp) REVERT: A 1445 ASN cc_start: 0.8651 (t0) cc_final: 0.8359 (t0) REVERT: A 1467 PHE cc_start: 0.7473 (m-80) cc_final: 0.7238 (m-80) REVERT: A 1653 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7666 (ttp) REVERT: A 1659 LEU cc_start: 0.8629 (mp) cc_final: 0.8405 (mp) REVERT: A 1767 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8184 (m-40) REVERT: A 1768 MET cc_start: 0.8528 (mmm) cc_final: 0.8215 (mmm) outliers start: 41 outliers final: 25 residues processed: 204 average time/residue: 0.0783 time to fit residues: 23.9204 Evaluate side-chains 194 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1238 LYS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1530 GLN Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1653 MET Chi-restraints excluded: chain A residue 1767 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.173592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139532 restraints weight = 12267.174| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.70 r_work: 0.3169 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9491 Z= 0.137 Angle : 0.621 12.916 12844 Z= 0.307 Chirality : 0.038 0.171 1486 Planarity : 0.004 0.057 1532 Dihedral : 13.366 123.763 1707 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.75 % Allowed : 24.18 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.26), residues: 1104 helix: 0.94 (0.18), residues: 798 sheet: -4.50 (1.03), residues: 12 loop : -1.76 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 812 TYR 0.016 0.001 TYR A1201 PHE 0.017 0.001 PHE A 260 TRP 0.019 0.001 TRP A1260 HIS 0.004 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9487) covalent geometry : angle 0.62071 (12836) SS BOND : bond 0.00194 ( 4) SS BOND : angle 1.17886 ( 8) hydrogen bonds : bond 0.03630 ( 600) hydrogen bonds : angle 4.29005 ( 1749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7052 (tp30) REVERT: A 223 ARG cc_start: 0.7329 (ptm-80) cc_final: 0.6960 (mtp-110) REVERT: A 366 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8356 (mp) REVERT: A 370 MET cc_start: 0.8690 (tmm) cc_final: 0.8429 (ttt) REVERT: A 705 MET cc_start: 0.6303 (mmp) cc_final: 0.4179 (tmm) REVERT: A 769 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6641 (tt) REVERT: A 777 TYR cc_start: 0.4665 (OUTLIER) cc_final: 0.3422 (m-80) REVERT: A 842 ASN cc_start: 0.7397 (p0) cc_final: 0.7010 (m-40) REVERT: A 901 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7456 (mt-10) REVERT: A 1212 PHE cc_start: 0.7456 (t80) cc_final: 0.7230 (t80) REVERT: A 1238 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7112 (tttt) REVERT: A 1255 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: A 1322 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.6944 (mpp) REVERT: A 1445 ASN cc_start: 0.8738 (t0) cc_final: 0.8450 (t0) REVERT: A 1659 LEU cc_start: 0.8669 (mp) cc_final: 0.8464 (mp) REVERT: A 1767 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8232 (m-40) REVERT: A 1768 MET cc_start: 0.8576 (mmm) cc_final: 0.8280 (mmm) outliers start: 45 outliers final: 29 residues processed: 200 average time/residue: 0.0767 time to fit residues: 22.7454 Evaluate side-chains 198 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1238 LYS Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1530 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1595 ILE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1730 CYS Chi-restraints excluded: chain A residue 1767 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 72 optimal weight: 0.0010 chunk 33 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 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 = 0.4008 r_free = 0.4008 target = 0.173679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138472 restraints weight = 12180.229| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.63 r_work: 0.3178 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9491 Z= 0.140 Angle : 0.649 11.254 12844 Z= 0.317 Chirality : 0.039 0.176 1486 Planarity : 0.004 0.058 1532 Dihedral : 13.081 122.561 1707 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.91 % Allowed : 24.39 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1104 helix: 0.95 (0.18), residues: 796 sheet: -4.46 (1.04), residues: 12 loop : -1.83 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 812 TYR 0.017 0.001 TYR A1683 PHE 0.013 0.001 PHE A1467 TRP 0.020 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9487) covalent geometry : angle 0.64899 (12836) SS BOND : bond 0.00195 ( 4) SS BOND : angle 1.20277 ( 8) hydrogen bonds : bond 0.03621 ( 600) hydrogen bonds : angle 4.31913 ( 1749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7110 (tp30) REVERT: A 223 ARG cc_start: 0.7397 (ptm-80) cc_final: 0.6889 (mtp-110) REVERT: A 255 MET cc_start: 0.8268 (tpp) cc_final: 0.8019 (mtm) REVERT: A 366 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 370 MET cc_start: 0.8681 (tmm) cc_final: 0.8414 (ttt) REVERT: A 705 MET cc_start: 0.6112 (mmp) cc_final: 0.4312 (tmm) REVERT: A 769 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6523 (tt) REVERT: A 777 TYR cc_start: 0.4568 (OUTLIER) cc_final: 0.3277 (m-80) REVERT: A 842 ASN cc_start: 0.7418 (p0) cc_final: 0.6903 (m-40) REVERT: A 901 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7454 (mt-10) REVERT: A 1212 PHE cc_start: 0.7505 (t80) cc_final: 0.7264 (t80) REVERT: A 1238 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7043 (tttt) REVERT: A 1322 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.6887 (mpp) REVERT: A 1445 ASN cc_start: 0.8738 (t0) cc_final: 0.8459 (t0) REVERT: A 1659 LEU cc_start: 0.8635 (mp) cc_final: 0.8401 (mp) REVERT: A 1767 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8178 (m-40) REVERT: A 1768 MET cc_start: 0.8581 (mmm) cc_final: 0.8284 (mmm) outliers start: 37 outliers final: 28 residues processed: 189 average time/residue: 0.0840 time to fit residues: 23.2820 Evaluate side-chains 195 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1238 LYS Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1530 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1595 ILE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1730 CYS Chi-restraints excluded: chain A residue 1767 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 0.0000 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 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 = 0.4025 r_free = 0.4025 target = 0.175444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141978 restraints weight = 12157.696| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.70 r_work: 0.3213 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9491 Z= 0.124 Angle : 0.644 12.566 12844 Z= 0.311 Chirality : 0.038 0.179 1486 Planarity : 0.004 0.056 1532 Dihedral : 12.612 120.625 1707 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.80 % Allowed : 24.29 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.26), residues: 1104 helix: 1.07 (0.18), residues: 796 sheet: -4.32 (1.10), residues: 12 loop : -1.82 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.017 0.001 TYR A1201 PHE 0.014 0.001 PHE A 260 TRP 0.017 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9487) covalent geometry : angle 0.64313 (12836) SS BOND : bond 0.00270 ( 4) SS BOND : angle 1.30814 ( 8) hydrogen bonds : bond 0.03509 ( 600) hydrogen bonds : angle 4.22411 ( 1749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7072 (tp30) REVERT: A 223 ARG cc_start: 0.7281 (ptm-80) cc_final: 0.6790 (mtp-110) REVERT: A 255 MET cc_start: 0.8354 (tpp) cc_final: 0.8083 (mtm) REVERT: A 366 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 370 MET cc_start: 0.8654 (tmm) cc_final: 0.8388 (ttt) REVERT: A 705 MET cc_start: 0.6158 (mmp) cc_final: 0.4360 (tmm) REVERT: A 769 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6460 (tt) REVERT: A 777 TYR cc_start: 0.4529 (OUTLIER) cc_final: 0.3289 (m-80) REVERT: A 842 ASN cc_start: 0.7420 (p0) cc_final: 0.6896 (m-40) REVERT: A 901 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 940 LEU cc_start: 0.9105 (mt) cc_final: 0.8824 (mp) REVERT: A 1212 PHE cc_start: 0.7448 (t80) cc_final: 0.7204 (t80) REVERT: A 1238 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7064 (tttt) REVERT: A 1322 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6880 (mpp) REVERT: A 1445 ASN cc_start: 0.8703 (t0) cc_final: 0.8442 (t0) REVERT: A 1659 LEU cc_start: 0.8622 (mp) cc_final: 0.8407 (mp) REVERT: A 1768 MET cc_start: 0.8576 (mmm) cc_final: 0.8287 (mmm) outliers start: 36 outliers final: 27 residues processed: 201 average time/residue: 0.0808 time to fit residues: 23.9635 Evaluate side-chains 194 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1238 LYS Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1530 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1730 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135879 restraints weight = 12149.092| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.82 r_work: 0.3150 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9491 Z= 0.171 Angle : 0.694 12.246 12844 Z= 0.338 Chirality : 0.041 0.186 1486 Planarity : 0.004 0.058 1532 Dihedral : 13.050 120.610 1707 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.38 % Allowed : 24.39 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.25), residues: 1104 helix: 0.93 (0.18), residues: 789 sheet: -4.48 (1.04), residues: 12 loop : -1.74 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 812 TYR 0.017 0.002 TYR A1683 PHE 0.016 0.001 PHE A 260 TRP 0.015 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9487) covalent geometry : angle 0.69276 (12836) SS BOND : bond 0.00258 ( 4) SS BOND : angle 1.67449 ( 8) hydrogen bonds : bond 0.03791 ( 600) hydrogen bonds : angle 4.39766 ( 1749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7098 (tp30) REVERT: A 366 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 370 MET cc_start: 0.8707 (tmm) cc_final: 0.8446 (ttt) REVERT: A 705 MET cc_start: 0.6265 (mmp) cc_final: 0.4755 (tmm) REVERT: A 769 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6496 (tt) REVERT: A 777 TYR cc_start: 0.4839 (OUTLIER) cc_final: 0.3306 (m-80) REVERT: A 842 ASN cc_start: 0.7495 (p0) cc_final: 0.6947 (m-40) REVERT: A 901 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 1212 PHE cc_start: 0.7470 (t80) cc_final: 0.7261 (t80) REVERT: A 1238 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7040 (tttt) REVERT: A 1322 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.6942 (mpp) REVERT: A 1659 LEU cc_start: 0.8666 (mp) cc_final: 0.8462 (mp) REVERT: A 1768 MET cc_start: 0.8623 (mmm) cc_final: 0.8303 (mmm) outliers start: 32 outliers final: 27 residues processed: 177 average time/residue: 0.0772 time to fit residues: 20.5541 Evaluate side-chains 185 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1238 LYS Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1530 GLN Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1730 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 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 = 0.4002 r_free = 0.4002 target = 0.172993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137088 restraints weight = 12117.834| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.80 r_work: 0.3154 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9491 Z= 0.156 Angle : 0.689 12.171 12844 Z= 0.334 Chirality : 0.040 0.183 1486 Planarity : 0.004 0.058 1532 Dihedral : 12.824 120.554 1707 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.48 % Allowed : 24.71 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1104 helix: 0.91 (0.18), residues: 793 sheet: -4.42 (1.07), residues: 12 loop : -1.82 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 812 TYR 0.017 0.002 TYR A1201 PHE 0.014 0.001 PHE A 260 TRP 0.015 0.001 TRP A1260 HIS 0.004 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9487) covalent geometry : angle 0.68836 (12836) SS BOND : bond 0.00247 ( 4) SS BOND : angle 1.40339 ( 8) hydrogen bonds : bond 0.03697 ( 600) hydrogen bonds : angle 4.35045 ( 1749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.28 seconds wall clock time: 39 minutes 32.25 seconds (2372.25 seconds total)