Starting phenix.real_space_refine on Tue Jul 29 10:31:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6klc_0706/07_2025/6klc_0706.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klc_0706/07_2025/6klc_0706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6klc_0706/07_2025/6klc_0706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klc_0706/07_2025/6klc_0706.map" model { file = "/net/cci-nas-00/data/ceres_data/6klc_0706/07_2025/6klc_0706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klc_0706/07_2025/6klc_0706.cif" } resolution = 3.9 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= 0.001 sd= 0.012 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 Mn 1 7.51 5 S 72 5.16 5 C 7134 2.51 5 N 1866 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 11210 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11209 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 41, 'TRANS': 1394} Chain breaks: 18 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 343 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 6, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 255 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.74, per 1000 atoms: 0.60 Number of scatterers: 11210 At special positions: 0 Unit cell: (119.68, 112.88, 125.12, 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) Mn 1 24.99 S 72 16.00 O 2137 8.00 N 1866 7.00 C 7134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 58.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 removed outlier: 3.603A pdb=" N ILE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.997A pdb=" N VAL A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 108 through 133 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 170 through 177 removed outlier: 4.282A pdb=" N SER A 174 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 232 through 249 removed outlier: 3.884A pdb=" N LEU A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.896A pdb=" N PHE A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.533A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 336 removed outlier: 4.241A pdb=" N MET A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.530A pdb=" N ARG A 398 " --> pdb=" O TRP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 411 No H-bonds generated for 'chain 'A' and resid 410 through 411' Processing helix chain 'A' and resid 415 through 415 No H-bonds generated for 'chain 'A' and resid 415 through 415' Processing helix chain 'A' and resid 416 through 436 removed outlier: 3.560A pdb=" N ASN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.725A pdb=" N ARG A 581 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE A 583 " --> pdb=" O LYS A 580 " (cutoff:3.500A) Proline residue: A 584 - end of helix Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 612 through 630 Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.564A pdb=" N GLN A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.791A pdb=" N LEU A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 709 Processing helix chain 'A' and resid 717 through 737 Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.555A pdb=" N LEU A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 795 Processing helix chain 'A' and resid 846 through 862 Processing helix chain 'A' and resid 870 through 886 removed outlier: 3.640A pdb=" N LEU A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 912 through 929 removed outlier: 3.563A pdb=" N GLU A 929 " --> pdb=" O ASP A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1098 removed outlier: 4.004A pdb=" N LEU A1098 " --> pdb=" O MET A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1159 Processing helix chain 'A' and resid 1167 through 1184 removed outlier: 3.608A pdb=" N MET A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1211 removed outlier: 3.532A pdb=" N PHE A1205 " --> pdb=" O CYS A1201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A1211 " --> pdb=" O THR A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1238 removed outlier: 3.848A pdb=" N LEU A1229 " --> pdb=" O GLY A1225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A1237 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A1238 " --> pdb=" O MET A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1270 through 1282 removed outlier: 3.646A pdb=" N GLY A1282 " --> pdb=" O ASN A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1323 Processing helix chain 'A' and resid 1340 through 1350 removed outlier: 3.515A pdb=" N THR A1344 " --> pdb=" O ASP A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1368 removed outlier: 3.642A pdb=" N PHE A1354 " --> pdb=" O ASP A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1408 removed outlier: 4.173A pdb=" N PHE A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1432 Processing helix chain 'A' and resid 1435 through 1452 removed outlier: 3.975A pdb=" N CYS A1439 " --> pdb=" O PRO A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1490 through 1506 removed outlier: 3.593A pdb=" N LYS A1494 " --> pdb=" O ASP A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1518 removed outlier: 4.395A pdb=" N PHE A1515 " --> pdb=" O LEU A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 Processing helix chain 'A' and resid 1580 through 1590 removed outlier: 4.232A pdb=" N LYS A1584 " --> pdb=" O PRO A1580 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A1590 " --> pdb=" O ILE A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1626 removed outlier: 3.670A pdb=" N GLY A1618 " --> pdb=" O SER A1614 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1619 " --> pdb=" O ILE A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1649 removed outlier: 3.773A pdb=" N ILE A1644 " --> pdb=" O TYR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1701 Processing helix chain 'A' and resid 1703 through 1707 Processing helix chain 'A' and resid 1742 through 1752 Processing helix chain 'A' and resid 1781 through 1788 Processing helix chain 'A' and resid 1797 through 1802 removed outlier: 3.807A pdb=" N VAL A1802 " --> pdb=" O VAL A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1820 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.003A pdb=" N LEU A 98 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 100 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 542 removed outlier: 3.557A pdb=" N PHE A 541 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1121 through 1126 removed outlier: 3.548A pdb=" N ARG A1133 " --> pdb=" O LYS A1126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1326 through 1330 removed outlier: 3.894A pdb=" N GLY A1379 " --> pdb=" O SER A1188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1241 through 1242 Processing sheet with id=AA6, first strand: chain 'A' and resid 1382 through 1385 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AA8, first strand: chain 'A' and resid 1631 through 1632 600 hydrogen bonds defined for protein. 1752 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: 4.18 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2957 1.33 - 1.45: 1968 1.45 - 1.57: 6361 1.57 - 1.70: 0 1.70 - 1.82: 109 Bond restraints: 11395 Sorted by residual: bond pdb=" N ASP A1334 " pdb=" CA ASP A1334 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.89e+00 bond pdb=" C VAL A1434 " pdb=" O VAL A1434 " ideal model delta sigma weight residual 1.240 1.213 0.027 1.26e-02 6.30e+03 4.48e+00 bond pdb=" N TYR A1452 " pdb=" CA TYR A1452 " ideal model delta sigma weight residual 1.458 1.430 0.027 1.33e-02 5.65e+03 4.12e+00 bond pdb=" CA ILE A 152 " pdb=" CB ILE A 152 " ideal model delta sigma weight residual 1.537 1.563 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" C TYR A1455 " pdb=" O TYR A1455 " ideal model delta sigma weight residual 1.246 1.231 0.015 9.20e-03 1.18e+04 2.72e+00 ... (remaining 11390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14610 1.41 - 2.82: 659 2.82 - 4.22: 99 4.22 - 5.63: 31 5.63 - 7.04: 11 Bond angle restraints: 15410 Sorted by residual: angle pdb=" C TYR A1455 " pdb=" N PRO A1456 " pdb=" CA PRO A1456 " ideal model delta sigma weight residual 119.84 126.53 -6.69 1.25e+00 6.40e-01 2.86e+01 angle pdb=" N VAL A 690 " pdb=" CA VAL A 690 " pdb=" C VAL A 690 " ideal model delta sigma weight residual 113.47 108.15 5.32 1.01e+00 9.80e-01 2.78e+01 angle pdb=" N VAL A1436 " pdb=" CA VAL A1436 " pdb=" C VAL A1436 " ideal model delta sigma weight residual 110.36 115.66 -5.30 1.05e+00 9.07e-01 2.54e+01 angle pdb=" N THR A1116 " pdb=" CA THR A1116 " pdb=" C THR A1116 " ideal model delta sigma weight residual 114.04 109.13 4.91 1.24e+00 6.50e-01 1.56e+01 angle pdb=" N TYR A1665 " pdb=" CA TYR A1665 " pdb=" C TYR A1665 " ideal model delta sigma weight residual 108.13 114.23 -6.10 1.72e+00 3.38e-01 1.26e+01 ... (remaining 15405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 6309 17.59 - 35.19: 506 35.19 - 52.78: 85 52.78 - 70.37: 13 70.37 - 87.96: 6 Dihedral angle restraints: 6919 sinusoidal: 2698 harmonic: 4221 Sorted by residual: dihedral pdb=" CA ARG A 336 " pdb=" C ARG A 336 " pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR A 706 " pdb=" C TYR A 706 " pdb=" N MET A 707 " pdb=" CA MET A 707 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ALA A 744 " pdb=" C ALA A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1653 0.071 - 0.143: 145 0.143 - 0.214: 10 0.214 - 0.286: 1 0.286 - 0.357: 1 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CA HIS A 443 " pdb=" N HIS A 443 " pdb=" C HIS A 443 " pdb=" CB HIS A 443 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA HIS A1437 " pdb=" N HIS A1437 " pdb=" C HIS A1437 " pdb=" CB HIS A1437 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN A1432 " pdb=" N ASN A1432 " pdb=" C ASN A1432 " pdb=" CB ASN A1432 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 1807 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1431 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ALA A1431 " -0.069 2.00e-02 2.50e+03 pdb=" O ALA A1431 " 0.026 2.00e-02 2.50e+03 pdb=" N ASN A1432 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1333 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C ASP A1333 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A1333 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A1334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 152 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 153 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.029 5.00e-02 4.00e+02 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1013 2.74 - 3.28: 11920 3.28 - 3.82: 17702 3.82 - 4.36: 20024 4.36 - 4.90: 34375 Nonbonded interactions: 85034 Sorted by model distance: nonbonded pdb=" O PRO A1459 " pdb=" NE2 GLN A1483 " model vdw 2.198 3.120 nonbonded pdb=" OE2 GLU A 731 " pdb=" OG1 THR A1271 " model vdw 2.217 3.040 nonbonded pdb=" O SER A 440 " pdb=" OG SER A 440 " model vdw 2.222 3.040 nonbonded pdb=" OD2 ASP A 89 " pdb=" N CYS A 103 " model vdw 2.281 3.120 nonbonded pdb=" NH1 ARG A 643 " pdb=" OH TYR A 706 " model vdw 2.282 3.120 ... (remaining 85029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.170 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.003 0.044 11395 Z= 0.168 Angle : 0.700 7.040 15410 Z= 0.426 Chirality : 0.043 0.357 1810 Planarity : 0.003 0.053 1949 Dihedral : 13.241 87.964 4165 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.30 % Favored : 90.49 % Rotamer: Outliers : 0.64 % Allowed : 5.06 % Favored : 94.30 % 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: -3.27 (0.19), residues: 1398 helix: -1.02 (0.16), residues: 789 sheet: -1.64 (0.49), residues: 108 loop : -4.21 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1704 HIS 0.005 0.001 HIS A 738 PHE 0.011 0.001 PHE A 104 TYR 0.014 0.001 TYR A 706 ARG 0.003 0.000 ARG A 643 Details of bonding type rmsd hydrogen bonds : bond 0.12718 ( 600) hydrogen bonds : angle 6.69663 ( 1752) covalent geometry : bond 0.00300 (11395) covalent geometry : angle 0.70029 (15410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 359 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.5901 (ttm) cc_final: 0.5571 (ttm) REVERT: A 113 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 114 GLN cc_start: 0.7941 (tp40) cc_final: 0.7684 (tt0) REVERT: A 115 LYS cc_start: 0.8041 (tptt) cc_final: 0.7423 (tptt) REVERT: A 118 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6421 (tm-30) REVERT: A 240 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 241 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 325 TRP cc_start: 0.7701 (m100) cc_final: 0.7179 (m100) REVERT: A 407 MET cc_start: 0.8844 (mmp) cc_final: 0.8114 (mmt) REVERT: A 448 MET cc_start: 0.7376 (tmm) cc_final: 0.7106 (tmm) REVERT: A 660 ASP cc_start: 0.7612 (t0) cc_final: 0.7253 (t0) REVERT: A 727 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 856 LEU cc_start: 0.9525 (tp) cc_final: 0.8910 (tp) REVERT: A 860 PHE cc_start: 0.7793 (m-80) cc_final: 0.7425 (m-80) REVERT: A 925 ASP cc_start: 0.8953 (t0) cc_final: 0.8688 (t0) REVERT: A 926 GLN cc_start: 0.9020 (pp30) cc_final: 0.8733 (pp30) REVERT: A 1094 MET cc_start: 0.3657 (pmm) cc_final: 0.3317 (pmm) REVERT: A 1151 ASP cc_start: 0.8649 (p0) cc_final: 0.8420 (p0) REVERT: A 1160 LEU cc_start: 0.9142 (mt) cc_final: 0.8917 (mp) REVERT: A 1242 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 1253 LYS cc_start: 0.8353 (tptp) cc_final: 0.8042 (mmtt) REVERT: A 1341 GLN cc_start: 0.8304 (pp30) cc_final: 0.7747 (pp30) REVERT: A 1364 MET cc_start: 0.7935 (mmm) cc_final: 0.7592 (tpp) REVERT: A 1436 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 1479 ARG cc_start: 0.7935 (mtt90) cc_final: 0.6928 (mtm180) REVERT: A 1485 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8210 (mm-30) REVERT: A 1551 ASN cc_start: 0.7951 (t0) cc_final: 0.7448 (t0) REVERT: A 1629 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7901 (mmtp) REVERT: A 1797 LEU cc_start: 0.6333 (mt) cc_final: 0.5891 (mm) outliers start: 8 outliers final: 5 residues processed: 365 average time/residue: 0.2509 time to fit residues: 126.8619 Evaluate side-chains 252 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 246 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1457 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0470 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 289 HIS A 758 ASN A 794 ASN A 869 ASN A1128 GLN A1132 ASN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 HIS A1287 HIS A1315 ASN A1409 ASN A1451 GLN A1475 ASN A1551 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.159323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120402 restraints weight = 20413.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123920 restraints weight = 12249.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126222 restraints weight = 8687.593| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11395 Z= 0.130 Angle : 0.676 9.784 15410 Z= 0.341 Chirality : 0.043 0.310 1810 Planarity : 0.004 0.039 1949 Dihedral : 5.242 53.533 1528 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.44 % Favored : 90.49 % Rotamer: Outliers : 2.49 % Allowed : 15.10 % Favored : 82.41 % 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: -1.93 (0.21), residues: 1398 helix: 0.18 (0.18), residues: 803 sheet: -1.10 (0.50), residues: 110 loop : -3.94 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 155 HIS 0.005 0.001 HIS A 213 PHE 0.019 0.002 PHE A 300 TYR 0.014 0.001 TYR A1665 ARG 0.008 0.001 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 600) hydrogen bonds : angle 4.48138 ( 1752) covalent geometry : bond 0.00270 (11395) covalent geometry : angle 0.67610 (15410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.6065 (ttm) cc_final: 0.5735 (ttm) REVERT: A 113 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 115 LYS cc_start: 0.8198 (tptt) cc_final: 0.7633 (tptt) REVERT: A 118 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6614 (tm-30) REVERT: A 240 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 241 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7469 (tt0) REVERT: A 323 GLN cc_start: 0.8665 (mp10) cc_final: 0.8413 (mp10) REVERT: A 325 TRP cc_start: 0.7556 (m100) cc_final: 0.7345 (m100) REVERT: A 335 MET cc_start: 0.7881 (pmm) cc_final: 0.7493 (pmm) REVERT: A 360 GLN cc_start: 0.6259 (OUTLIER) cc_final: 0.6053 (pp30) REVERT: A 407 MET cc_start: 0.8864 (mmp) cc_final: 0.8462 (mmt) REVERT: A 599 MET cc_start: 0.9259 (mtm) cc_final: 0.8953 (mtm) REVERT: A 657 ASP cc_start: 0.7155 (t0) cc_final: 0.6669 (t0) REVERT: A 660 ASP cc_start: 0.7394 (t0) cc_final: 0.6953 (t0) REVERT: A 727 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8083 (tm-30) REVERT: A 856 LEU cc_start: 0.9547 (tp) cc_final: 0.8880 (tp) REVERT: A 860 PHE cc_start: 0.7925 (m-80) cc_final: 0.7526 (m-80) REVERT: A 881 MET cc_start: 0.8310 (mtm) cc_final: 0.8103 (mtm) REVERT: A 925 ASP cc_start: 0.8916 (t0) cc_final: 0.8702 (t0) REVERT: A 926 GLN cc_start: 0.9000 (pp30) cc_final: 0.8757 (pp30) REVERT: A 1094 MET cc_start: 0.3840 (pmm) cc_final: 0.3419 (pmm) REVERT: A 1120 LYS cc_start: 0.8709 (tttm) cc_final: 0.8379 (tttp) REVERT: A 1151 ASP cc_start: 0.8778 (p0) cc_final: 0.8471 (p0) REVERT: A 1240 MET cc_start: 0.6318 (ttm) cc_final: 0.5714 (tmm) REVERT: A 1242 GLU cc_start: 0.7856 (mm-30) cc_final: 0.6897 (mm-30) REVERT: A 1253 LYS cc_start: 0.8336 (tptp) cc_final: 0.8112 (mmtt) REVERT: A 1341 GLN cc_start: 0.8140 (pp30) cc_final: 0.7724 (pp30) REVERT: A 1454 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8102 (mmp-170) REVERT: A 1460 PHE cc_start: 0.8540 (m-10) cc_final: 0.8285 (m-80) REVERT: A 1479 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7241 (mtt180) REVERT: A 1485 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8234 (mt-10) REVERT: A 1551 ASN cc_start: 0.8005 (t0) cc_final: 0.7421 (t0) REVERT: A 1629 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7912 (mmtp) REVERT: A 1693 ILE cc_start: 0.8540 (mm) cc_final: 0.8339 (mm) outliers start: 31 outliers final: 16 residues processed: 301 average time/residue: 0.2179 time to fit residues: 95.8891 Evaluate side-chains 264 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 246 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1499 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 104 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN A1664 GLN A1800 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.159165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120319 restraints weight = 20599.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123871 restraints weight = 12231.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126212 restraints weight = 8632.778| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11395 Z= 0.123 Angle : 0.659 10.336 15410 Z= 0.329 Chirality : 0.043 0.245 1810 Planarity : 0.004 0.038 1949 Dihedral : 5.079 52.464 1525 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.51 % Favored : 90.41 % Rotamer: Outliers : 3.37 % Allowed : 16.47 % Favored : 80.16 % 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: -1.23 (0.22), residues: 1398 helix: 0.76 (0.18), residues: 798 sheet: -0.63 (0.51), residues: 107 loop : -3.67 (0.23), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 155 HIS 0.009 0.001 HIS A 213 PHE 0.016 0.001 PHE A 799 TYR 0.017 0.001 TYR A 552 ARG 0.007 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 600) hydrogen bonds : angle 4.15972 ( 1752) covalent geometry : bond 0.00260 (11395) covalent geometry : angle 0.65948 (15410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.6201 (ttm) cc_final: 0.5851 (ttm) REVERT: A 113 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7115 (mm-30) REVERT: A 114 GLN cc_start: 0.7702 (pt0) cc_final: 0.7034 (pp30) REVERT: A 115 LYS cc_start: 0.8171 (tptt) cc_final: 0.7870 (tptt) REVERT: A 118 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6763 (tp30) REVERT: A 240 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 302 TYR cc_start: 0.8006 (m-80) cc_final: 0.7740 (m-80) REVERT: A 323 GLN cc_start: 0.8651 (mp10) cc_final: 0.8423 (mp10) REVERT: A 407 MET cc_start: 0.8903 (mmp) cc_final: 0.8468 (mmt) REVERT: A 599 MET cc_start: 0.9354 (mtm) cc_final: 0.8916 (mtm) REVERT: A 657 ASP cc_start: 0.7269 (t0) cc_final: 0.6767 (t0) REVERT: A 660 ASP cc_start: 0.7419 (t0) cc_final: 0.6977 (t0) REVERT: A 727 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 856 LEU cc_start: 0.9549 (tp) cc_final: 0.8857 (tp) REVERT: A 860 PHE cc_start: 0.8134 (m-80) cc_final: 0.7712 (m-80) REVERT: A 881 MET cc_start: 0.8256 (mtm) cc_final: 0.7974 (mtm) REVERT: A 925 ASP cc_start: 0.8951 (t0) cc_final: 0.8713 (t0) REVERT: A 1094 MET cc_start: 0.4110 (pmm) cc_final: 0.3664 (pmm) REVERT: A 1151 ASP cc_start: 0.8801 (p0) cc_final: 0.8476 (p0) REVERT: A 1240 MET cc_start: 0.6006 (ttm) cc_final: 0.5336 (tmm) REVERT: A 1242 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7077 (mm-30) REVERT: A 1253 LYS cc_start: 0.8380 (tptp) cc_final: 0.8147 (mmtt) REVERT: A 1301 ASN cc_start: 0.8497 (m110) cc_final: 0.8204 (m-40) REVERT: A 1341 GLN cc_start: 0.8069 (pp30) cc_final: 0.7507 (pp30) REVERT: A 1344 THR cc_start: 0.9238 (p) cc_final: 0.9026 (t) REVERT: A 1479 ARG cc_start: 0.7753 (mtt90) cc_final: 0.7365 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 1551 ASN cc_start: 0.8075 (t0) cc_final: 0.7464 (t0) outliers start: 42 outliers final: 25 residues processed: 293 average time/residue: 0.2136 time to fit residues: 92.4000 Evaluate side-chains 266 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1623 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 79 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 GLN A 795 ASN A1236 HIS A1409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115247 restraints weight = 20613.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118619 restraints weight = 12500.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120825 restraints weight = 8952.700| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11395 Z= 0.178 Angle : 0.707 13.013 15410 Z= 0.353 Chirality : 0.045 0.346 1810 Planarity : 0.004 0.037 1949 Dihedral : 4.846 28.808 1519 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.73 % Favored : 90.20 % Rotamer: Outliers : 3.53 % Allowed : 18.63 % Favored : 77.83 % 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: -1.07 (0.23), residues: 1398 helix: 0.83 (0.18), residues: 805 sheet: -0.65 (0.51), residues: 107 loop : -3.52 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 325 HIS 0.007 0.001 HIS A 213 PHE 0.023 0.002 PHE A 423 TYR 0.024 0.002 TYR A1665 ARG 0.010 0.001 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 600) hydrogen bonds : angle 4.28467 ( 1752) covalent geometry : bond 0.00402 (11395) covalent geometry : angle 0.70704 (15410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7235 (mt-10) REVERT: A 114 GLN cc_start: 0.7769 (pt0) cc_final: 0.7363 (pp30) REVERT: A 115 LYS cc_start: 0.8333 (tptt) cc_final: 0.7602 (tmtt) REVERT: A 325 TRP cc_start: 0.7595 (m100) cc_final: 0.7274 (m100) REVERT: A 407 MET cc_start: 0.8891 (mmp) cc_final: 0.8502 (mmt) REVERT: A 493 THR cc_start: 0.9182 (m) cc_final: 0.8980 (m) REVERT: A 660 ASP cc_start: 0.7527 (t0) cc_final: 0.7283 (t0) REVERT: A 727 GLU cc_start: 0.8689 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 856 LEU cc_start: 0.9549 (tp) cc_final: 0.8908 (tp) REVERT: A 860 PHE cc_start: 0.8151 (m-80) cc_final: 0.7775 (m-80) REVERT: A 881 MET cc_start: 0.8349 (mtm) cc_final: 0.7896 (mtm) REVERT: A 917 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8822 (mmmt) REVERT: A 925 ASP cc_start: 0.8971 (t0) cc_final: 0.8757 (t0) REVERT: A 926 GLN cc_start: 0.9052 (pp30) cc_final: 0.8793 (pp30) REVERT: A 1094 MET cc_start: 0.4155 (pmm) cc_final: 0.3660 (pmm) REVERT: A 1151 ASP cc_start: 0.8840 (p0) cc_final: 0.8558 (p0) REVERT: A 1240 MET cc_start: 0.5868 (ttm) cc_final: 0.5304 (tmm) REVERT: A 1242 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 1253 LYS cc_start: 0.8426 (tptp) cc_final: 0.8204 (mmtt) REVERT: A 1301 ASN cc_start: 0.8612 (m110) cc_final: 0.8305 (m-40) REVERT: A 1341 GLN cc_start: 0.8124 (pp30) cc_final: 0.7495 (pp30) REVERT: A 1344 THR cc_start: 0.9273 (p) cc_final: 0.9061 (t) REVERT: A 1479 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7475 (mtt-85) REVERT: A 1485 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8229 (mt-10) REVERT: A 1551 ASN cc_start: 0.8276 (t0) cc_final: 0.7706 (t0) REVERT: A 1560 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8231 (mtm) outliers start: 44 outliers final: 36 residues processed: 276 average time/residue: 0.2026 time to fit residues: 83.2627 Evaluate side-chains 271 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1560 MET Chi-restraints excluded: chain A residue 1623 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 94 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.0370 chunk 59 optimal weight: 0.0010 chunk 46 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.158809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120069 restraints weight = 20402.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123520 restraints weight = 12452.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125821 restraints weight = 8915.513| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11395 Z= 0.118 Angle : 0.669 13.255 15410 Z= 0.332 Chirality : 0.043 0.329 1810 Planarity : 0.003 0.038 1949 Dihedral : 4.653 24.360 1518 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.80 % Favored : 91.13 % Rotamer: Outliers : 2.81 % Allowed : 19.76 % Favored : 77.43 % 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: -0.79 (0.23), residues: 1398 helix: 1.08 (0.18), residues: 802 sheet: -0.55 (0.51), residues: 100 loop : -3.39 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 325 HIS 0.007 0.001 HIS A 213 PHE 0.015 0.001 PHE A 423 TYR 0.013 0.001 TYR A1665 ARG 0.009 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 600) hydrogen bonds : angle 3.98970 ( 1752) covalent geometry : bond 0.00247 (11395) covalent geometry : angle 0.66886 (15410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7403 (mt-10) REVERT: A 114 GLN cc_start: 0.7804 (pt0) cc_final: 0.7332 (pp30) REVERT: A 115 LYS cc_start: 0.8123 (tptt) cc_final: 0.7289 (tmtt) REVERT: A 323 GLN cc_start: 0.8381 (mp10) cc_final: 0.7639 (pm20) REVERT: A 407 MET cc_start: 0.8836 (mmp) cc_final: 0.8505 (mmt) REVERT: A 493 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8838 (m) REVERT: A 578 ASP cc_start: 0.7885 (t0) cc_final: 0.7365 (m-30) REVERT: A 602 TRP cc_start: 0.8744 (OUTLIER) cc_final: 0.8388 (m-10) REVERT: A 657 ASP cc_start: 0.7231 (t0) cc_final: 0.6775 (t0) REVERT: A 660 ASP cc_start: 0.7492 (t0) cc_final: 0.7085 (t0) REVERT: A 727 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 856 LEU cc_start: 0.9521 (tp) cc_final: 0.8803 (tp) REVERT: A 860 PHE cc_start: 0.8130 (m-80) cc_final: 0.7765 (m-80) REVERT: A 917 LYS cc_start: 0.9241 (mmmt) cc_final: 0.8790 (mmmt) REVERT: A 925 ASP cc_start: 0.8907 (t0) cc_final: 0.8694 (t0) REVERT: A 926 GLN cc_start: 0.9040 (pp30) cc_final: 0.8806 (pp30) REVERT: A 1094 MET cc_start: 0.4336 (pmm) cc_final: 0.4076 (ptt) REVERT: A 1151 ASP cc_start: 0.8785 (p0) cc_final: 0.8471 (p0) REVERT: A 1301 ASN cc_start: 0.8508 (m110) cc_final: 0.8239 (m-40) REVERT: A 1341 GLN cc_start: 0.8138 (pp30) cc_final: 0.7514 (pp30) REVERT: A 1344 THR cc_start: 0.9261 (p) cc_final: 0.9022 (t) REVERT: A 1485 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8214 (mt-10) REVERT: A 1551 ASN cc_start: 0.8120 (t0) cc_final: 0.7558 (t0) REVERT: A 1629 LYS cc_start: 0.8467 (mmtt) cc_final: 0.7829 (mmtp) outliers start: 35 outliers final: 24 residues processed: 276 average time/residue: 0.2117 time to fit residues: 86.4155 Evaluate side-chains 262 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1409 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 = 0.4049 r_free = 0.4049 target = 0.158021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118807 restraints weight = 20695.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122360 restraints weight = 12453.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124687 restraints weight = 8858.136| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11395 Z= 0.129 Angle : 0.703 12.656 15410 Z= 0.347 Chirality : 0.045 0.386 1810 Planarity : 0.004 0.037 1949 Dihedral : 4.644 24.461 1518 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.23 % Favored : 90.70 % Rotamer: Outliers : 3.13 % Allowed : 21.20 % Favored : 75.66 % 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: -0.77 (0.23), residues: 1398 helix: 1.09 (0.18), residues: 803 sheet: -0.46 (0.51), residues: 100 loop : -3.39 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 325 HIS 0.009 0.001 HIS A1287 PHE 0.011 0.001 PHE A 423 TYR 0.028 0.001 TYR A 552 ARG 0.010 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 600) hydrogen bonds : angle 4.09854 ( 1752) covalent geometry : bond 0.00284 (11395) covalent geometry : angle 0.70303 (15410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8225 (mp0) cc_final: 0.7837 (pm20) REVERT: A 91 TYR cc_start: 0.4118 (p90) cc_final: 0.3777 (p90) REVERT: A 113 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7305 (mt-10) REVERT: A 115 LYS cc_start: 0.8105 (tptt) cc_final: 0.7241 (tmtt) REVERT: A 323 GLN cc_start: 0.8424 (mp10) cc_final: 0.7978 (pm20) REVERT: A 325 TRP cc_start: 0.7427 (m100) cc_final: 0.7220 (m100) REVERT: A 381 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4687 (mm) REVERT: A 407 MET cc_start: 0.8867 (mmp) cc_final: 0.8500 (mmt) REVERT: A 435 ARG cc_start: 0.8282 (tpm170) cc_final: 0.7862 (ttm-80) REVERT: A 493 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8760 (m) REVERT: A 578 ASP cc_start: 0.7989 (t0) cc_final: 0.7509 (m-30) REVERT: A 602 TRP cc_start: 0.8771 (OUTLIER) cc_final: 0.8380 (m-10) REVERT: A 657 ASP cc_start: 0.7235 (t0) cc_final: 0.6760 (t0) REVERT: A 660 ASP cc_start: 0.7565 (t0) cc_final: 0.7147 (t0) REVERT: A 727 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8130 (tm-30) REVERT: A 856 LEU cc_start: 0.9540 (tp) cc_final: 0.8848 (tp) REVERT: A 860 PHE cc_start: 0.8139 (m-80) cc_final: 0.7774 (m-80) REVERT: A 917 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8848 (mmmt) REVERT: A 925 ASP cc_start: 0.8942 (t0) cc_final: 0.8728 (t0) REVERT: A 1094 MET cc_start: 0.4396 (pmm) cc_final: 0.4149 (ptt) REVERT: A 1151 ASP cc_start: 0.8776 (p0) cc_final: 0.8420 (p0) REVERT: A 1237 MET cc_start: 0.8493 (tpp) cc_final: 0.8207 (mmt) REVERT: A 1252 MET cc_start: 0.8551 (mmm) cc_final: 0.8300 (mmm) REVERT: A 1301 ASN cc_start: 0.8681 (m110) cc_final: 0.8374 (m-40) REVERT: A 1338 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8834 (mt) REVERT: A 1341 GLN cc_start: 0.8112 (pp30) cc_final: 0.7457 (pp30) REVERT: A 1344 THR cc_start: 0.9278 (p) cc_final: 0.9057 (t) REVERT: A 1479 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8099 (mtm-85) REVERT: A 1485 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8231 (mt-10) REVERT: A 1551 ASN cc_start: 0.8233 (t0) cc_final: 0.7695 (t0) REVERT: A 1629 LYS cc_start: 0.8533 (mmtt) cc_final: 0.7855 (mmtp) outliers start: 39 outliers final: 30 residues processed: 264 average time/residue: 0.2668 time to fit residues: 105.1256 Evaluate side-chains 264 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1560 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 0.0050 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 ASN ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.156153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117887 restraints weight = 20777.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120680 restraints weight = 13343.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122422 restraints weight = 8796.635| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11395 Z= 0.140 Angle : 0.702 16.052 15410 Z= 0.349 Chirality : 0.044 0.307 1810 Planarity : 0.004 0.042 1949 Dihedral : 4.676 23.384 1518 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.16 % Favored : 90.77 % Rotamer: Outliers : 3.37 % Allowed : 21.85 % Favored : 74.78 % 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: -0.67 (0.23), residues: 1398 helix: 1.16 (0.18), residues: 805 sheet: -0.27 (0.51), residues: 94 loop : -3.35 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 325 HIS 0.011 0.001 HIS A 213 PHE 0.013 0.001 PHE A1305 TYR 0.021 0.001 TYR A 552 ARG 0.011 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 600) hydrogen bonds : angle 4.05464 ( 1752) covalent geometry : bond 0.00314 (11395) covalent geometry : angle 0.70156 (15410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8473 (mp0) cc_final: 0.8227 (pm20) REVERT: A 91 TYR cc_start: 0.4282 (p90) cc_final: 0.4001 (p90) REVERT: A 113 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 115 LYS cc_start: 0.8081 (tptt) cc_final: 0.7175 (tmtt) REVERT: A 323 GLN cc_start: 0.8453 (mp10) cc_final: 0.8022 (pm20) REVERT: A 325 TRP cc_start: 0.7585 (m100) cc_final: 0.7380 (m100) REVERT: A 407 MET cc_start: 0.8938 (mmp) cc_final: 0.8541 (mmt) REVERT: A 435 ARG cc_start: 0.8282 (tpm170) cc_final: 0.7722 (ttm-80) REVERT: A 493 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8735 (m) REVERT: A 602 TRP cc_start: 0.8886 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: A 657 ASP cc_start: 0.7209 (t0) cc_final: 0.6741 (t0) REVERT: A 660 ASP cc_start: 0.7717 (t0) cc_final: 0.7336 (t0) REVERT: A 693 MET cc_start: 0.7351 (tmm) cc_final: 0.6605 (ptp) REVERT: A 694 MET cc_start: 0.8287 (tpt) cc_final: 0.7553 (tpt) REVERT: A 727 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 856 LEU cc_start: 0.9532 (tp) cc_final: 0.8897 (tp) REVERT: A 860 PHE cc_start: 0.8069 (m-80) cc_final: 0.7711 (m-80) REVERT: A 917 LYS cc_start: 0.9265 (mmmt) cc_final: 0.8834 (mmmt) REVERT: A 926 GLN cc_start: 0.9073 (pp30) cc_final: 0.8576 (pp30) REVERT: A 1151 ASP cc_start: 0.8749 (p0) cc_final: 0.8402 (p0) REVERT: A 1252 MET cc_start: 0.8473 (mmm) cc_final: 0.8257 (mmm) REVERT: A 1301 ASN cc_start: 0.8709 (m110) cc_final: 0.8400 (m-40) REVERT: A 1338 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8854 (mt) REVERT: A 1341 GLN cc_start: 0.8160 (pp30) cc_final: 0.7481 (pp30) REVERT: A 1485 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8280 (mt-10) REVERT: A 1551 ASN cc_start: 0.8326 (t0) cc_final: 0.7849 (t0) REVERT: A 1629 LYS cc_start: 0.8551 (mmtt) cc_final: 0.7883 (mmtp) outliers start: 42 outliers final: 34 residues processed: 264 average time/residue: 0.2043 time to fit residues: 80.1956 Evaluate side-chains 263 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1560 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1409 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 = 0.4013 r_free = 0.4013 target = 0.154981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115405 restraints weight = 20649.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118784 restraints weight = 12614.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121003 restraints weight = 9055.390| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11395 Z= 0.155 Angle : 0.735 15.921 15410 Z= 0.366 Chirality : 0.045 0.314 1810 Planarity : 0.003 0.037 1949 Dihedral : 4.699 24.866 1517 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.44 % Favored : 90.49 % Rotamer: Outliers : 3.21 % Allowed : 23.53 % Favored : 73.25 % 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: -0.73 (0.23), residues: 1398 helix: 1.10 (0.18), residues: 806 sheet: -0.43 (0.51), residues: 100 loop : -3.37 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 325 HIS 0.008 0.001 HIS A 213 PHE 0.016 0.001 PHE A 423 TYR 0.019 0.001 TYR A1665 ARG 0.007 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 600) hydrogen bonds : angle 4.18417 ( 1752) covalent geometry : bond 0.00351 (11395) covalent geometry : angle 0.73491 (15410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TYR cc_start: 0.4559 (p90) cc_final: 0.4354 (p90) REVERT: A 115 LYS cc_start: 0.8100 (tptt) cc_final: 0.7181 (tmtt) REVERT: A 323 GLN cc_start: 0.8458 (mp10) cc_final: 0.8070 (pm20) REVERT: A 325 TRP cc_start: 0.7617 (m100) cc_final: 0.7354 (m100) REVERT: A 388 LYS cc_start: 0.8381 (mptt) cc_final: 0.7811 (mptt) REVERT: A 407 MET cc_start: 0.8673 (mmp) cc_final: 0.8425 (mmt) REVERT: A 435 ARG cc_start: 0.8204 (tpm170) cc_final: 0.7664 (ttm-80) REVERT: A 493 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8749 (m) REVERT: A 578 ASP cc_start: 0.7819 (t0) cc_final: 0.7302 (m-30) REVERT: A 602 TRP cc_start: 0.8916 (OUTLIER) cc_final: 0.8201 (m-10) REVERT: A 657 ASP cc_start: 0.7233 (t0) cc_final: 0.6709 (t0) REVERT: A 660 ASP cc_start: 0.7730 (t0) cc_final: 0.7347 (t0) REVERT: A 727 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 856 LEU cc_start: 0.9540 (tp) cc_final: 0.8962 (tp) REVERT: A 860 PHE cc_start: 0.8188 (m-80) cc_final: 0.7836 (m-80) REVERT: A 917 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8828 (mmmt) REVERT: A 926 GLN cc_start: 0.9058 (pp30) cc_final: 0.8830 (pp30) REVERT: A 1237 MET cc_start: 0.8618 (tpp) cc_final: 0.8263 (mmt) REVERT: A 1252 MET cc_start: 0.8462 (mmm) cc_final: 0.8099 (mmm) REVERT: A 1301 ASN cc_start: 0.8597 (m110) cc_final: 0.8306 (m-40) REVERT: A 1338 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8866 (mt) REVERT: A 1341 GLN cc_start: 0.8155 (pp30) cc_final: 0.7430 (pp30) REVERT: A 1485 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8278 (mt-10) REVERT: A 1551 ASN cc_start: 0.8197 (t0) cc_final: 0.7706 (t0) REVERT: A 1629 LYS cc_start: 0.8570 (mmtt) cc_final: 0.7913 (mmtp) outliers start: 40 outliers final: 33 residues processed: 261 average time/residue: 0.2009 time to fit residues: 77.7583 Evaluate side-chains 262 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1560 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 0.0040 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.157465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117988 restraints weight = 20662.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121405 restraints weight = 12454.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123778 restraints weight = 8926.679| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11395 Z= 0.128 Angle : 0.735 16.549 15410 Z= 0.363 Chirality : 0.045 0.271 1810 Planarity : 0.003 0.039 1949 Dihedral : 4.656 23.091 1517 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.08 % Favored : 90.84 % Rotamer: Outliers : 2.81 % Allowed : 23.86 % Favored : 73.33 % 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: -0.65 (0.23), residues: 1398 helix: 1.16 (0.18), residues: 808 sheet: -0.08 (0.53), residues: 88 loop : -3.33 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 325 HIS 0.009 0.001 HIS A 213 PHE 0.015 0.001 PHE A1305 TYR 0.016 0.001 TYR A 552 ARG 0.012 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 600) hydrogen bonds : angle 4.07262 ( 1752) covalent geometry : bond 0.00279 (11395) covalent geometry : angle 0.73538 (15410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8148 (tptt) cc_final: 0.7214 (tmtt) REVERT: A 323 GLN cc_start: 0.8342 (mp10) cc_final: 0.8094 (pm20) REVERT: A 325 TRP cc_start: 0.7794 (m100) cc_final: 0.7586 (m100) REVERT: A 407 MET cc_start: 0.8669 (mmp) cc_final: 0.8409 (mmt) REVERT: A 435 ARG cc_start: 0.8146 (tpm170) cc_final: 0.7693 (ttm-80) REVERT: A 493 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8695 (m) REVERT: A 578 ASP cc_start: 0.7826 (t0) cc_final: 0.7343 (m-30) REVERT: A 602 TRP cc_start: 0.8851 (OUTLIER) cc_final: 0.8271 (m-10) REVERT: A 657 ASP cc_start: 0.7161 (t0) cc_final: 0.6612 (t0) REVERT: A 660 ASP cc_start: 0.7686 (t0) cc_final: 0.7310 (t0) REVERT: A 693 MET cc_start: 0.7649 (tmm) cc_final: 0.6796 (ptp) REVERT: A 727 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 856 LEU cc_start: 0.9537 (tp) cc_final: 0.9034 (tp) REVERT: A 860 PHE cc_start: 0.8170 (m-80) cc_final: 0.7853 (m-80) REVERT: A 872 ASP cc_start: 0.8716 (t0) cc_final: 0.8511 (t0) REVERT: A 917 LYS cc_start: 0.9270 (mmmt) cc_final: 0.8793 (mmmt) REVERT: A 1237 MET cc_start: 0.8619 (tpp) cc_final: 0.8290 (mmt) REVERT: A 1252 MET cc_start: 0.8438 (mmm) cc_final: 0.8082 (mmm) REVERT: A 1301 ASN cc_start: 0.8559 (m110) cc_final: 0.8280 (m-40) REVERT: A 1338 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8837 (mt) REVERT: A 1341 GLN cc_start: 0.8056 (pp30) cc_final: 0.7309 (pp30) REVERT: A 1485 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8159 (mt-10) REVERT: A 1502 LEU cc_start: 0.8876 (tp) cc_final: 0.8384 (pp) REVERT: A 1519 TYR cc_start: 0.7598 (t80) cc_final: 0.6429 (t80) REVERT: A 1551 ASN cc_start: 0.8230 (t0) cc_final: 0.7739 (t0) outliers start: 35 outliers final: 28 residues processed: 257 average time/residue: 0.2011 time to fit residues: 77.0546 Evaluate side-chains 260 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 27 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116702 restraints weight = 20581.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120143 restraints weight = 12475.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122425 restraints weight = 8924.652| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11395 Z= 0.141 Angle : 0.762 16.718 15410 Z= 0.376 Chirality : 0.045 0.289 1810 Planarity : 0.003 0.038 1949 Dihedral : 4.664 23.804 1517 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.51 % Favored : 90.41 % Rotamer: Outliers : 2.81 % Allowed : 23.61 % Favored : 73.57 % 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: -0.65 (0.23), residues: 1398 helix: 1.15 (0.18), residues: 807 sheet: -0.39 (0.51), residues: 100 loop : -3.31 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 325 HIS 0.008 0.001 HIS A 213 PHE 0.015 0.001 PHE A1460 TYR 0.016 0.001 TYR A1665 ARG 0.014 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 600) hydrogen bonds : angle 4.12196 ( 1752) covalent geometry : bond 0.00316 (11395) covalent geometry : angle 0.76199 (15410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4516 (tmm) cc_final: 0.4249 (ppp) REVERT: A 323 GLN cc_start: 0.8301 (mp10) cc_final: 0.7965 (pm20) REVERT: A 325 TRP cc_start: 0.7915 (m100) cc_final: 0.7664 (m100) REVERT: A 407 MET cc_start: 0.8685 (mmp) cc_final: 0.8410 (mmt) REVERT: A 435 ARG cc_start: 0.8158 (tpm170) cc_final: 0.7728 (ttm-80) REVERT: A 493 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8705 (m) REVERT: A 510 MET cc_start: 0.8322 (tpp) cc_final: 0.8031 (tpp) REVERT: A 578 ASP cc_start: 0.7841 (t0) cc_final: 0.7300 (m-30) REVERT: A 602 TRP cc_start: 0.8893 (OUTLIER) cc_final: 0.8294 (m-10) REVERT: A 657 ASP cc_start: 0.7200 (t0) cc_final: 0.6624 (t0) REVERT: A 660 ASP cc_start: 0.7732 (t0) cc_final: 0.7367 (t0) REVERT: A 661 LYS cc_start: 0.8197 (tptt) cc_final: 0.7947 (tptm) REVERT: A 727 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8212 (tm-30) REVERT: A 856 LEU cc_start: 0.9533 (tp) cc_final: 0.9050 (tp) REVERT: A 860 PHE cc_start: 0.8171 (m-80) cc_final: 0.7863 (m-80) REVERT: A 872 ASP cc_start: 0.8698 (t0) cc_final: 0.8493 (t0) REVERT: A 917 LYS cc_start: 0.9250 (mmmt) cc_final: 0.8779 (mmmt) REVERT: A 1237 MET cc_start: 0.8602 (tpp) cc_final: 0.8255 (mmt) REVERT: A 1252 MET cc_start: 0.8382 (mmm) cc_final: 0.8060 (mmm) REVERT: A 1301 ASN cc_start: 0.8615 (m110) cc_final: 0.8300 (m-40) REVERT: A 1338 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8866 (mt) REVERT: A 1341 GLN cc_start: 0.8084 (pp30) cc_final: 0.7327 (pp30) REVERT: A 1485 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 1551 ASN cc_start: 0.8258 (t0) cc_final: 0.7780 (t0) outliers start: 35 outliers final: 30 residues processed: 244 average time/residue: 0.2045 time to fit residues: 75.2094 Evaluate side-chains 255 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1439 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 10 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 0.0030 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 358 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.157843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118934 restraints weight = 20328.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122445 restraints weight = 12300.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124745 restraints weight = 8753.260| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11395 Z= 0.130 Angle : 0.762 16.841 15410 Z= 0.375 Chirality : 0.045 0.318 1810 Planarity : 0.003 0.038 1949 Dihedral : 4.622 23.296 1517 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.16 % Favored : 90.77 % Rotamer: Outliers : 2.57 % Allowed : 24.42 % Favored : 73.01 % 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: -0.60 (0.23), residues: 1398 helix: 1.18 (0.18), residues: 809 sheet: -0.22 (0.52), residues: 94 loop : -3.28 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 155 HIS 0.009 0.001 HIS A 213 PHE 0.014 0.001 PHE A1305 TYR 0.016 0.001 TYR A 214 ARG 0.014 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 600) hydrogen bonds : angle 4.06972 ( 1752) covalent geometry : bond 0.00284 (11395) covalent geometry : angle 0.76156 (15410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3775.21 seconds wall clock time: 66 minutes 57.85 seconds (4017.85 seconds total)