Starting phenix.real_space_refine on Mon Jul 28 01:38:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fbs_31519/07_2025/7fbs_31519.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fbs_31519/07_2025/7fbs_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_31519/07_2025/7fbs_31519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fbs_31519/07_2025/7fbs_31519.map" model { file = "/net/cci-nas-00/data/ceres_data/7fbs_31519/07_2025/7fbs_31519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fbs_31519/07_2025/7fbs_31519.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 3} 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-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 6.29, per 1000 atoms: 0.68 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: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.90 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: 2.60 Time building geometry restraints manager: 2.79 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: 2.240 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.820 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- 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 : 18.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP A 882 HIS 0.006 0.001 HIS A 739 PHE 0.020 0.002 PHE A1452 TYR 0.018 0.003 TYR A1447 ARG 0.005 0.001 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.13170 ( 600) hydrogen bonds : angle 6.89160 ( 1749) SS BOND : bond 0.00341 ( 4) SS BOND : angle 1.90336 ( 8) covalent geometry : bond 0.02156 ( 9487) covalent geometry : angle 1.19894 (12836) *********************** 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 : 0.920 Fit side-chains 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: 0.7399 (mmt90) REVERT: A 1532 PHE cc_start: 0.8101 (t80) cc_final: 0.7706 (t80) REVERT: A 1594 ASN cc_start: 0.8025 (m110) cc_final: 0.7698 (m-40) REVERT: A 1603 LEU cc_start: 0.8688 (mt) cc_final: 0.8452 (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: 0.2235 time to fit residues: 74.3361 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 : 0.978 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.0040 chunk 46 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.4690 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.173653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138040 restraints weight = 11996.467| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.83 r_work: 0.3162 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9491 Z= 0.138 Angle : 0.639 13.651 12844 Z= 0.319 Chirality : 0.039 0.154 1486 Planarity : 0.004 0.059 1532 Dihedral : 17.251 142.493 1732 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.70 % Allowed : 20.80 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.24), residues: 1104 helix: -0.24 (0.17), residues: 791 sheet: -4.65 (1.21), residues: 12 loop : -2.02 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 823 HIS 0.002 0.001 HIS A 739 PHE 0.014 0.001 PHE A1598 TYR 0.015 0.001 TYR A1411 ARG 0.005 0.000 ARG A1318 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 600) hydrogen bonds : angle 4.80405 ( 1749) SS BOND : bond 0.00546 ( 4) SS BOND : angle 1.58123 ( 8) covalent geometry : bond 0.00308 ( 9487) covalent geometry : angle 0.63766 (12836) *********************** 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 232 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7865 (tmtt) REVERT: A 223 ARG cc_start: 0.7258 (ptm-80) cc_final: 0.6964 (mtp-110) REVERT: A 370 MET cc_start: 0.8679 (tmm) cc_final: 0.8378 (ttt) REVERT: A 705 MET cc_start: 0.5273 (mmp) cc_final: 0.3667 (tmm) REVERT: A 749 MET cc_start: 0.8658 (tmm) cc_final: 0.8365 (tmm) REVERT: A 842 ASN cc_start: 0.7586 (p0) cc_final: 0.7122 (m-40) REVERT: A 940 LEU cc_start: 0.9101 (mt) cc_final: 0.8883 (mp) REVERT: A 1198 LYS cc_start: 0.6677 (mmpt) cc_final: 0.6340 (ptpt) REVERT: A 1212 PHE cc_start: 0.7335 (t80) cc_final: 0.7011 (t80) REVERT: A 1302 LYS cc_start: 0.8353 (pttm) cc_final: 0.8112 (pttm) REVERT: A 1547 MET cc_start: 0.7692 (ttm) cc_final: 0.7462 (ttp) outliers start: 35 outliers final: 14 residues processed: 222 average time/residue: 0.2496 time to fit residues: 78.2605 Evaluate side-chains 174 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 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 15 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** A 731 ASN A 871 HIS ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1594 ASN A1736 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.172299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136926 restraints weight = 12207.074| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.77 r_work: 0.3151 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9491 Z= 0.160 Angle : 0.626 9.331 12844 Z= 0.317 Chirality : 0.039 0.138 1486 Planarity : 0.004 0.058 1532 Dihedral : 15.622 133.800 1711 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.54 % Allowed : 21.01 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1104 helix: 0.43 (0.18), residues: 786 sheet: -4.52 (1.15), residues: 12 loop : -1.93 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 PHE 0.013 0.001 PHE A1404 TYR 0.013 0.001 TYR A1447 ARG 0.003 0.000 ARG A1628 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 600) hydrogen bonds : angle 4.62315 ( 1749) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.51577 ( 8) covalent geometry : bond 0.00370 ( 9487) covalent geometry : angle 0.62479 (12836) *********************** 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 220 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7065 (tp30) REVERT: A 223 ARG cc_start: 0.7485 (ptm-80) cc_final: 0.7098 (mtp-110) REVERT: A 370 MET cc_start: 0.8643 (tmm) cc_final: 0.8344 (ttt) REVERT: A 705 MET cc_start: 0.5289 (mmp) cc_final: 0.3574 (tmm) REVERT: A 749 MET cc_start: 0.8631 (tmm) cc_final: 0.8342 (tmm) REVERT: A 769 ILE cc_start: 0.6764 (mt) cc_final: 0.6345 (mt) REVERT: A 777 TYR cc_start: 0.4452 (OUTLIER) cc_final: 0.3624 (m-80) REVERT: A 842 ASN cc_start: 0.7598 (p0) cc_final: 0.7021 (m-40) REVERT: A 1198 LYS cc_start: 0.6795 (mmpt) cc_final: 0.6415 (ptpt) REVERT: A 1212 PHE cc_start: 0.7375 (t80) cc_final: 0.7043 (t80) REVERT: A 1298 MET cc_start: 0.5894 (ppp) cc_final: 0.5550 (ppp) REVERT: A 1302 LYS cc_start: 0.8321 (pttm) cc_final: 0.8076 (pttm) REVERT: A 1322 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7108 (mpp) REVERT: A 1547 MET cc_start: 0.7605 (ttm) cc_final: 0.7286 (ttp) REVERT: A 1610 LEU cc_start: 0.8633 (mt) cc_final: 0.8075 (tt) REVERT: A 1640 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7622 (ttm-80) REVERT: A 1767 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8270 (m-40) REVERT: A 1768 MET cc_start: 0.8578 (mmm) cc_final: 0.8213 (mmm) outliers start: 43 outliers final: 20 residues processed: 205 average time/residue: 0.2003 time to fit residues: 59.3271 Evaluate side-chains 185 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN 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 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 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 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 Chi-restraints excluded: chain A residue 1774 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 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 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** 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 = 0.3991 r_free = 0.3991 target = 0.172279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137539 restraints weight = 12062.021| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.65 r_work: 0.3188 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9491 Z= 0.155 Angle : 0.623 12.568 12844 Z= 0.312 Chirality : 0.039 0.138 1486 Planarity : 0.004 0.059 1532 Dihedral : 14.924 132.626 1709 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.01 % Allowed : 23.02 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1104 helix: 0.60 (0.18), residues: 793 sheet: -4.50 (1.08), residues: 12 loop : -1.76 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 PHE 0.013 0.001 PHE A1404 TYR 0.013 0.001 TYR A1447 ARG 0.004 0.000 ARG A 812 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 600) hydrogen bonds : angle 4.53828 ( 1749) SS BOND : bond 0.00261 ( 4) SS BOND : angle 1.40940 ( 8) covalent geometry : bond 0.00358 ( 9487) covalent geometry : angle 0.62268 (12836) *********************** 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 213 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.941 Fit side-chains REVERT: A 162 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7059 (tp30) REVERT: A 223 ARG cc_start: 0.7342 (ptm-80) cc_final: 0.6956 (mtp-110) REVERT: A 370 MET cc_start: 0.8648 (tmm) cc_final: 0.8399 (ttt) REVERT: A 705 MET cc_start: 0.5773 (mmp) cc_final: 0.3771 (tmm) REVERT: A 749 MET cc_start: 0.8661 (tmm) cc_final: 0.8388 (tmm) REVERT: A 769 ILE cc_start: 0.6804 (mt) cc_final: 0.6415 (mt) REVERT: A 772 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7186 (pt) REVERT: A 777 TYR cc_start: 0.4492 (OUTLIER) cc_final: 0.3627 (m-80) REVERT: A 842 ASN cc_start: 0.7542 (p0) cc_final: 0.7072 (m-40) REVERT: A 1198 LYS cc_start: 0.6752 (mmpt) cc_final: 0.6440 (ptpt) REVERT: A 1212 PHE cc_start: 0.7393 (t80) cc_final: 0.7072 (t80) REVERT: A 1298 MET cc_start: 0.6146 (ppp) cc_final: 0.5914 (ppp) REVERT: A 1302 LYS cc_start: 0.8342 (pttm) cc_final: 0.8096 (pttm) REVERT: A 1322 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7010 (mpp) REVERT: A 1467 PHE cc_start: 0.7288 (m-80) cc_final: 0.7065 (m-80) REVERT: A 1576 GLU cc_start: 0.7304 (pt0) cc_final: 0.7027 (pt0) REVERT: A 1767 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8246 (m-40) REVERT: A 1768 MET cc_start: 0.8539 (mmm) cc_final: 0.8209 (mmm) outliers start: 38 outliers final: 20 residues processed: 199 average time/residue: 0.2182 time to fit residues: 63.8273 Evaluate side-chains 185 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 421 ASN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 777 TYR 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 913 SER 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 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 1512 ILE Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1590 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** A1439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.140080 restraints weight = 12051.875| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.52 r_work: 0.3205 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9491 Z= 0.148 Angle : 0.604 9.169 12844 Z= 0.303 Chirality : 0.039 0.158 1486 Planarity : 0.004 0.057 1532 Dihedral : 14.278 126.341 1707 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.54 % Allowed : 23.13 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1104 helix: 0.74 (0.18), residues: 793 sheet: -4.54 (1.04), residues: 12 loop : -1.84 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1423 HIS 0.003 0.001 HIS A 739 PHE 0.012 0.001 PHE A1404 TYR 0.014 0.001 TYR A 417 ARG 0.005 0.000 ARG A 812 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 600) hydrogen bonds : angle 4.47749 ( 1749) SS BOND : bond 0.00235 ( 4) SS BOND : angle 1.30712 ( 8) covalent geometry : bond 0.00340 ( 9487) covalent geometry : angle 0.60361 (12836) *********************** 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 217 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7031 (tp30) REVERT: A 223 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.6857 (mtp-110) REVERT: A 370 MET cc_start: 0.8596 (tmm) cc_final: 0.8331 (ttt) REVERT: A 705 MET cc_start: 0.6069 (mmp) cc_final: 0.3998 (tmm) REVERT: A 749 MET cc_start: 0.8646 (tmm) cc_final: 0.8389 (tmm) REVERT: A 769 ILE cc_start: 0.6615 (mt) cc_final: 0.6302 (mt) REVERT: A 772 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7199 (pt) REVERT: A 777 TYR cc_start: 0.4345 (OUTLIER) cc_final: 0.3131 (m-80) REVERT: A 842 ASN cc_start: 0.7447 (p0) cc_final: 0.6918 (m-40) REVERT: A 1212 PHE cc_start: 0.7316 (t80) cc_final: 0.7003 (t80) REVERT: A 1298 MET cc_start: 0.6079 (ppp) cc_final: 0.5571 (ppp) REVERT: A 1302 LYS cc_start: 0.8276 (pttm) cc_final: 0.8067 (pttm) REVERT: A 1322 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.6878 (mpp) REVERT: A 1467 PHE cc_start: 0.7316 (m-80) cc_final: 0.7105 (m-80) REVERT: A 1576 GLU cc_start: 0.7481 (pt0) cc_final: 0.7252 (pt0) REVERT: A 1767 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8216 (m-40) REVERT: A 1768 MET cc_start: 0.8557 (mmm) cc_final: 0.8241 (mmm) outliers start: 43 outliers final: 25 residues processed: 205 average time/residue: 0.1915 time to fit residues: 57.4593 Evaluate side-chains 194 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 772 LEU Chi-restraints excluded: chain A residue 777 TYR 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 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 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 65 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 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** A 865 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.172891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139359 restraints weight = 12044.836| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.67 r_work: 0.3188 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9491 Z= 0.151 Angle : 0.621 13.030 12844 Z= 0.308 Chirality : 0.039 0.164 1486 Planarity : 0.004 0.058 1532 Dihedral : 13.933 125.945 1707 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.44 % Allowed : 24.18 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1104 helix: 0.80 (0.18), residues: 794 sheet: -4.65 (0.97), residues: 12 loop : -1.78 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 PHE 0.012 0.001 PHE A1404 TYR 0.014 0.001 TYR A 417 ARG 0.004 0.000 ARG A 812 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 600) hydrogen bonds : angle 4.47192 ( 1749) SS BOND : bond 0.00242 ( 4) SS BOND : angle 1.34611 ( 8) covalent geometry : bond 0.00350 ( 9487) covalent geometry : angle 0.61998 (12836) *********************** 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 208 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7067 (tp30) REVERT: A 223 ARG cc_start: 0.7271 (ptm-80) cc_final: 0.6850 (mtp-110) REVERT: A 366 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 370 MET cc_start: 0.8637 (tmm) cc_final: 0.8376 (ttt) REVERT: A 705 MET cc_start: 0.6224 (mmp) cc_final: 0.4162 (tmm) REVERT: A 749 MET cc_start: 0.8635 (tmm) cc_final: 0.8371 (tmm) REVERT: A 769 ILE cc_start: 0.6583 (mt) cc_final: 0.6272 (mt) REVERT: A 777 TYR cc_start: 0.4299 (OUTLIER) cc_final: 0.3078 (m-80) REVERT: A 842 ASN cc_start: 0.7444 (p0) cc_final: 0.6928 (m-40) REVERT: A 1212 PHE cc_start: 0.7403 (t80) cc_final: 0.7073 (t80) REVERT: A 1238 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7039 (tttt) REVERT: A 1298 MET cc_start: 0.6023 (ppp) cc_final: 0.5553 (ppp) REVERT: A 1322 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6915 (mpp) REVERT: A 1467 PHE cc_start: 0.7421 (m-80) cc_final: 0.7216 (m-80) REVERT: A 1576 GLU cc_start: 0.7654 (pt0) cc_final: 0.7321 (pt0) REVERT: A 1767 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8188 (m-40) REVERT: A 1768 MET cc_start: 0.8540 (mmm) cc_final: 0.8237 (mmm) outliers start: 42 outliers final: 27 residues processed: 198 average time/residue: 0.1961 time to fit residues: 57.5808 Evaluate side-chains 190 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 772 LEU Chi-restraints excluded: chain A residue 777 TYR 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 913 SER 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 1406 ASN 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 1767 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 0.0670 chunk 100 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.175320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142504 restraints weight = 12220.822| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.76 r_work: 0.3217 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9491 Z= 0.118 Angle : 0.605 11.257 12844 Z= 0.297 Chirality : 0.038 0.165 1486 Planarity : 0.004 0.055 1532 Dihedral : 13.166 123.704 1707 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.12 % Allowed : 25.03 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1104 helix: 0.97 (0.18), residues: 794 sheet: -4.47 (1.04), residues: 12 loop : -1.81 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 PHE 0.017 0.001 PHE A 260 TYR 0.017 0.001 TYR A1201 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 600) hydrogen bonds : angle 4.29973 ( 1749) SS BOND : bond 0.00178 ( 4) SS BOND : angle 1.21303 ( 8) covalent geometry : bond 0.00256 ( 9487) covalent geometry : angle 0.60432 (12836) *********************** 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 216 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7117 (tp30) REVERT: A 223 ARG cc_start: 0.7295 (ptm-80) cc_final: 0.6859 (mtp-110) REVERT: A 705 MET cc_start: 0.6068 (mmp) cc_final: 0.4292 (tmm) REVERT: A 749 MET cc_start: 0.8568 (tmm) cc_final: 0.8352 (tmm) REVERT: A 769 ILE cc_start: 0.6381 (mt) cc_final: 0.6162 (mt) REVERT: A 777 TYR cc_start: 0.4188 (OUTLIER) cc_final: 0.3153 (m-80) REVERT: A 842 ASN cc_start: 0.7383 (p0) cc_final: 0.6878 (m-40) REVERT: A 940 LEU cc_start: 0.9093 (mt) cc_final: 0.8823 (mp) REVERT: A 1198 LYS cc_start: 0.6625 (mmpt) cc_final: 0.6402 (ptpt) REVERT: A 1212 PHE cc_start: 0.7427 (t80) cc_final: 0.7208 (t80) REVERT: A 1238 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7122 (tttt) REVERT: A 1302 LYS cc_start: 0.8396 (pttm) cc_final: 0.8196 (pttm) REVERT: A 1322 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6886 (mpp) REVERT: A 1467 PHE cc_start: 0.7459 (m-80) cc_final: 0.7225 (m-80) REVERT: A 1767 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8159 (m-40) outliers start: 39 outliers final: 24 residues processed: 204 average time/residue: 0.1832 time to fit residues: 54.9643 Evaluate side-chains 190 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 879 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 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 56 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 108 optimal weight: 0.0040 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.174035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137431 restraints weight = 12266.512| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.62 r_work: 0.3181 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9491 Z= 0.140 Angle : 0.655 13.684 12844 Z= 0.317 Chirality : 0.039 0.189 1486 Planarity : 0.004 0.057 1532 Dihedral : 13.085 122.853 1707 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.01 % Allowed : 24.71 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1104 helix: 0.97 (0.18), residues: 795 sheet: -4.46 (1.03), residues: 12 loop : -1.86 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 PHE 0.011 0.001 PHE A 394 TYR 0.017 0.001 TYR A1683 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 600) hydrogen bonds : angle 4.33264 ( 1749) SS BOND : bond 0.00166 ( 4) SS BOND : angle 1.16991 ( 8) covalent geometry : bond 0.00322 ( 9487) covalent geometry : angle 0.65419 (12836) *********************** 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 193 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7131 (tp30) REVERT: A 223 ARG cc_start: 0.7391 (ptm-80) cc_final: 0.6882 (mtp-110) REVERT: A 255 MET cc_start: 0.8338 (tpp) cc_final: 0.8071 (tpt) REVERT: A 303 ASN cc_start: 0.3752 (t0) cc_final: 0.3524 (m110) REVERT: A 366 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8366 (mp) REVERT: A 705 MET cc_start: 0.6039 (mmp) cc_final: 0.4324 (tmm) REVERT: A 749 MET cc_start: 0.8644 (tmm) cc_final: 0.8379 (tmm) REVERT: A 769 ILE cc_start: 0.6441 (mt) cc_final: 0.6203 (mt) REVERT: A 777 TYR cc_start: 0.4076 (OUTLIER) cc_final: 0.2996 (m-80) REVERT: A 842 ASN cc_start: 0.7456 (p0) cc_final: 0.6934 (m-40) REVERT: A 1198 LYS cc_start: 0.6780 (mmpt) cc_final: 0.6439 (ptpt) REVERT: A 1212 PHE cc_start: 0.7504 (t80) cc_final: 0.7297 (t80) REVERT: A 1238 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7076 (tttt) REVERT: A 1302 LYS cc_start: 0.8392 (pttm) cc_final: 0.8182 (pttm) REVERT: A 1322 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6753 (mpp) REVERT: A 1467 PHE cc_start: 0.7534 (m-80) cc_final: 0.7305 (m-80) REVERT: A 1576 GLU cc_start: 0.7747 (pt0) cc_final: 0.7278 (pt0) REVERT: A 1767 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8165 (m-40) REVERT: A 1768 MET cc_start: 0.8626 (mmm) cc_final: 0.8264 (mmm) outliers start: 38 outliers final: 25 residues processed: 183 average time/residue: 0.2424 time to fit residues: 64.6620 Evaluate side-chains 181 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 879 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 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 79 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.175357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141375 restraints weight = 12091.859| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.76 r_work: 0.3196 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9491 Z= 0.128 Angle : 0.648 12.182 12844 Z= 0.312 Chirality : 0.039 0.176 1486 Planarity : 0.004 0.056 1532 Dihedral : 12.684 120.999 1707 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.06 % Allowed : 25.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1104 helix: 1.07 (0.18), residues: 795 sheet: -4.35 (1.07), residues: 12 loop : -1.92 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 PHE 0.015 0.001 PHE A 260 TYR 0.018 0.001 TYR A1683 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 600) hydrogen bonds : angle 4.25959 ( 1749) SS BOND : bond 0.00239 ( 4) SS BOND : angle 1.29758 ( 8) covalent geometry : bond 0.00289 ( 9487) covalent geometry : angle 0.64750 (12836) *********************** 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 187 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7080 (tp30) REVERT: A 223 ARG cc_start: 0.7316 (ptm-80) cc_final: 0.6820 (mtp-110) REVERT: A 303 ASN cc_start: 0.4030 (t0) cc_final: 0.3616 (m110) REVERT: A 305 LEU cc_start: 0.7620 (tp) cc_final: 0.7273 (mt) REVERT: A 366 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 705 MET cc_start: 0.6209 (mmp) cc_final: 0.4527 (tmm) REVERT: A 749 MET cc_start: 0.8608 (tmm) cc_final: 0.8390 (tmm) REVERT: A 769 ILE cc_start: 0.6386 (mt) cc_final: 0.6160 (mt) REVERT: A 777 TYR cc_start: 0.4183 (OUTLIER) cc_final: 0.3112 (m-80) REVERT: A 842 ASN cc_start: 0.7446 (p0) cc_final: 0.6939 (m-40) REVERT: A 940 LEU cc_start: 0.9136 (mt) cc_final: 0.8856 (mp) REVERT: A 1238 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7160 (tttt) REVERT: A 1302 LYS cc_start: 0.8253 (pttm) cc_final: 0.8029 (pttm) REVERT: A 1322 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7008 (mpp) REVERT: A 1473 ASP cc_start: 0.8302 (m-30) cc_final: 0.7900 (t70) REVERT: A 1576 GLU cc_start: 0.7721 (pt0) cc_final: 0.7126 (pt0) REVERT: A 1768 MET cc_start: 0.8695 (mmm) cc_final: 0.8397 (mmm) outliers start: 29 outliers final: 23 residues processed: 179 average time/residue: 0.1940 time to fit residues: 50.3426 Evaluate side-chains 178 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 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 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 78 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 75 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 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** A1736 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.173837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139851 restraints weight = 12268.154| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.69 r_work: 0.3190 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9491 Z= 0.149 Angle : 0.670 12.555 12844 Z= 0.323 Chirality : 0.039 0.181 1486 Planarity : 0.004 0.057 1532 Dihedral : 12.769 120.203 1707 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.96 % Allowed : 25.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1104 helix: 0.99 (0.18), residues: 794 sheet: -4.43 (1.06), residues: 12 loop : -1.92 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 PHE 0.016 0.001 PHE A 260 TYR 0.021 0.001 TYR A1683 ARG 0.006 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 600) hydrogen bonds : angle 4.32411 ( 1749) SS BOND : bond 0.00212 ( 4) SS BOND : angle 1.45983 ( 8) covalent geometry : bond 0.00349 ( 9487) covalent geometry : angle 0.66940 (12836) ********************** 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 181 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7526 (mm110) REVERT: A 162 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7053 (tp30) REVERT: A 255 MET cc_start: 0.8152 (mmm) cc_final: 0.7866 (mtm) REVERT: A 303 ASN cc_start: 0.4161 (t0) cc_final: 0.3759 (m110) REVERT: A 305 LEU cc_start: 0.7574 (tp) cc_final: 0.7298 (mt) REVERT: A 366 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 705 MET cc_start: 0.6255 (mmp) cc_final: 0.4781 (tmm) REVERT: A 749 MET cc_start: 0.8647 (tmm) cc_final: 0.8391 (tmm) REVERT: A 769 ILE cc_start: 0.6454 (mt) cc_final: 0.6206 (mt) REVERT: A 777 TYR cc_start: 0.4232 (OUTLIER) cc_final: 0.3064 (m-80) REVERT: A 842 ASN cc_start: 0.7484 (p0) cc_final: 0.6963 (m-40) REVERT: A 1238 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7114 (tttt) REVERT: A 1302 LYS cc_start: 0.8326 (pttm) cc_final: 0.8091 (pttm) REVERT: A 1322 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6955 (mpp) REVERT: A 1473 ASP cc_start: 0.8183 (m-30) cc_final: 0.7839 (t70) REVERT: A 1576 GLU cc_start: 0.7659 (pt0) cc_final: 0.7374 (pt0) REVERT: A 1768 MET cc_start: 0.8585 (mmm) cc_final: 0.8258 (mmm) outliers start: 28 outliers final: 23 residues processed: 173 average time/residue: 0.1818 time to fit residues: 46.0244 Evaluate side-chains 176 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 772 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 843 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 1316 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 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 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 0.0000 chunk 92 optimal weight: 0.0010 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 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 = 0.4024 r_free = 0.4024 target = 0.175371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140877 restraints weight = 12160.983| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.75 r_work: 0.3202 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9491 Z= 0.129 Angle : 0.654 11.948 12844 Z= 0.316 Chirality : 0.039 0.182 1486 Planarity : 0.004 0.056 1532 Dihedral : 12.420 118.863 1707 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.17 % Allowed : 24.50 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1104 helix: 1.09 (0.18), residues: 793 sheet: -4.17 (1.17), residues: 12 loop : -1.91 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1260 HIS 0.003 0.001 HIS A 739 PHE 0.014 0.001 PHE A 260 TYR 0.019 0.001 TYR A1683 ARG 0.006 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 600) hydrogen bonds : angle 4.23714 ( 1749) SS BOND : bond 0.00206 ( 4) SS BOND : angle 1.18148 ( 8) covalent geometry : bond 0.00293 ( 9487) covalent geometry : angle 0.65354 (12836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5019.83 seconds wall clock time: 91 minutes 2.67 seconds (5462.67 seconds total)