Starting phenix.real_space_refine on Sat Jul 20 12:32:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qh3_18397/07_2024/8qh3_18397_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qh3_18397/07_2024/8qh3_18397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qh3_18397/07_2024/8qh3_18397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qh3_18397/07_2024/8qh3_18397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qh3_18397/07_2024/8qh3_18397_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qh3_18397/07_2024/8qh3_18397_neut.cif" } resolution = 2.81 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= 0.065 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 6907 2.51 5 N 1815 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1137": "OE1" <-> "OE2" Residue "A GLU 1237": "OE1" <-> "OE2" Residue "A GLU 1275": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10796 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1310, 10556 Classifications: {'peptide': 1310} Link IDs: {'PTRANS': 43, 'TRANS': 1266} Chain breaks: 5 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.07, per 1000 atoms: 0.65 Number of scatterers: 10796 At special positions: 0 Unit cell: (94.807, 99.841, 121.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 11 15.00 Mg 1 11.99 O 2004 8.00 N 1815 7.00 C 6907 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 - 3.50 Amino acid : False - 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: 4.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 58.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.740A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 409 through 428 removed outlier: 3.564A pdb=" N GLN A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.616A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.835A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 654 through 674 Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.657A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 760 removed outlier: 3.725A pdb=" N ALA A 739 " --> pdb=" O MET A 735 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 777 through 780 removed outlier: 3.644A pdb=" N ALA A 780 " --> pdb=" O ALA A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 777 through 780' Processing helix chain 'A' and resid 786 through 802 removed outlier: 4.015A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 929 through 946 removed outlier: 3.870A pdb=" N LEU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 992 removed outlier: 4.044A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1116 through 1126 Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 3.553A pdb=" N ASN A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.923A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1193 removed outlier: 3.943A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1218 Processing helix chain 'A' and resid 1221 through 1240 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 3.543A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1321 Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1385 removed outlier: 3.717A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1388 No H-bonds generated for 'chain 'A' and resid 1386 through 1388' Processing helix chain 'A' and resid 1389 through 1396 Processing helix chain 'A' and resid 1400 through 1408 removed outlier: 4.196A pdb=" N GLN A1403 " --> pdb=" O SER A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 Processing helix chain 'A' and resid 1443 through 1457 Processing helix chain 'A' and resid 1460 through 1471 removed outlier: 3.561A pdb=" N TRP A1464 " --> pdb=" O LYS A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1512 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.587A pdb=" N ASP A1540 " --> pdb=" O LYS A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1564 Proline residue: A1561 - end of helix removed outlier: 3.804A pdb=" N TYR A1564 " --> pdb=" O ALA A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1592 removed outlier: 3.926A pdb=" N CYS A1586 " --> pdb=" O ALA A1582 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A1587 " --> pdb=" O GLU A1583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.674A pdb=" N ASP A1099 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.365A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 893 through 897 removed outlier: 7.040A pdb=" N ALA A 877 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE A1018 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA A 879 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1168 through 1171 Processing sheet with id=AA9, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB1, first strand: chain 'A' and resid 1474 through 1479 removed outlier: 4.263A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1485 through 1489 596 hydrogen bonds defined for protein. 1668 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: 4.21 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3325 1.34 - 1.46: 2022 1.46 - 1.58: 5597 1.58 - 1.70: 21 1.70 - 1.82: 97 Bond restraints: 11062 Sorted by residual: bond pdb=" CE1 HIS A 957 " pdb=" NE2 HIS A 957 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.59e+01 bond pdb=" CA SER A 715 " pdb=" CB SER A 715 " ideal model delta sigma weight residual 1.529 1.482 0.047 1.55e-02 4.16e+03 9.05e+00 bond pdb=" N LYS A 876 " pdb=" CA LYS A 876 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.28e+00 bond pdb=" N ILE A 960 " pdb=" CA ILE A 960 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.60e+00 bond pdb=" N ILE A 952 " pdb=" CA ILE A 952 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.43e+00 ... (remaining 11057 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.57: 329 106.57 - 113.42: 5995 113.42 - 120.28: 4022 120.28 - 127.13: 4508 127.13 - 133.99: 147 Bond angle restraints: 15001 Sorted by residual: angle pdb=" CA GLN A 875 " pdb=" C GLN A 875 " pdb=" O GLN A 875 " ideal model delta sigma weight residual 121.87 117.70 4.17 1.10e+00 8.26e-01 1.44e+01 angle pdb=" CA ASN A 956 " pdb=" C ASN A 956 " pdb=" O ASN A 956 " ideal model delta sigma weight residual 122.64 117.96 4.68 1.25e+00 6.40e-01 1.40e+01 angle pdb=" C3' A C 2 " pdb=" O3' A C 2 " pdb=" P G C 3 " ideal model delta sigma weight residual 120.20 114.73 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C GLN A1412 " pdb=" N HIS A1413 " pdb=" CA HIS A1413 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.63e+00 angle pdb=" CA ARG A 961 " pdb=" C ARG A 961 " pdb=" O ARG A 961 " ideal model delta sigma weight residual 121.87 118.42 3.45 1.16e+00 7.43e-01 8.83e+00 ... (remaining 14996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 6258 29.79 - 59.59: 348 59.59 - 89.38: 30 89.38 - 119.18: 1 119.18 - 148.97: 1 Dihedral angle restraints: 6638 sinusoidal: 2780 harmonic: 3858 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 51.03 148.97 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" CA MET A1246 " pdb=" C MET A1246 " pdb=" N VAL A1247 " pdb=" CA VAL A1247 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A1092 " pdb=" CG GLU A1092 " pdb=" CD GLU A1092 " pdb=" OE1 GLU A1092 " ideal model delta sinusoidal sigma weight residual 0.00 -89.86 89.86 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1643 0.110 - 0.220: 31 0.220 - 0.331: 0 0.331 - 0.441: 0 0.441 - 0.551: 1 Chirality restraints: 1675 Sorted by residual: chirality pdb=" P A C 2 " pdb=" OP1 A C 2 " pdb=" OP2 A C 2 " pdb=" O5' A C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" CA ILE A 952 " pdb=" N ILE A 952 " pdb=" C ILE A 952 " pdb=" CB ILE A 952 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE A 960 " pdb=" N ILE A 960 " pdb=" C ILE A 960 " pdb=" CB ILE A 960 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 1672 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1503 " 0.052 5.00e-02 4.00e+02 7.77e-02 9.66e+00 pdb=" N PRO A1504 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A1504 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1504 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 961 " -0.272 9.50e-02 1.11e+02 1.22e-01 9.12e+00 pdb=" NE ARG A 961 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 961 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 961 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 961 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 904 " 0.266 9.50e-02 1.11e+02 1.19e-01 8.74e+00 pdb=" NE ARG A 904 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 904 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 904 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 904 " 0.009 2.00e-02 2.50e+03 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 100 2.61 - 3.18: 9243 3.18 - 3.76: 17605 3.76 - 4.33: 25326 4.33 - 4.90: 40832 Nonbonded interactions: 93106 Sorted by model distance: nonbonded pdb=" OD1 ASP A1099 " pdb="MG MG A2201 " model vdw 2.038 2.170 nonbonded pdb=" N GLU A1275 " pdb=" OE1 GLU A1275 " model vdw 2.188 2.520 nonbonded pdb=" OD2 ASP A 544 " pdb=" OG1 THR A 545 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR A 855 " pdb=" OE1 GLU A 871 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR A 302 " pdb=" OD2 ASP A 481 " model vdw 2.252 2.440 ... (remaining 93101 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.400 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: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.000 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.048 11062 Z= 0.205 Angle : 0.553 8.452 15001 Z= 0.312 Chirality : 0.042 0.551 1675 Planarity : 0.006 0.122 1848 Dihedral : 17.219 148.971 4140 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.16 % Allowed : 23.02 % Favored : 74.83 % 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: 0.67 (0.24), residues: 1298 helix: 1.11 (0.20), residues: 714 sheet: 0.26 (0.53), residues: 93 loop : -0.40 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 473 HIS 0.005 0.001 HIS A1413 PHE 0.016 0.001 PHE A 894 TYR 0.014 0.001 TYR A 912 ARG 0.004 0.000 ARG A1405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.112 Fit side-chains REVERT: A 280 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7088 (mm110) outliers start: 25 outliers final: 8 residues processed: 220 average time/residue: 1.2722 time to fit residues: 301.4530 Evaluate side-chains 170 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1592 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.0570 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 GLN A1058 GLN A1078 GLN A1122 GLN A1268 ASN A1364 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11062 Z= 0.188 Angle : 0.517 7.836 15001 Z= 0.272 Chirality : 0.039 0.131 1675 Planarity : 0.004 0.052 1848 Dihedral : 9.229 150.393 1591 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.40 % Allowed : 20.86 % Favored : 74.74 % 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: 1.02 (0.24), residues: 1298 helix: 1.50 (0.20), residues: 717 sheet: 0.51 (0.53), residues: 93 loop : -0.46 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.005 0.001 HIS A1413 PHE 0.044 0.002 PHE A 959 TYR 0.016 0.001 TYR A 912 ARG 0.003 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 269 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7132 (tp30) REVERT: A 728 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: A 902 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7365 (mmp-170) REVERT: A 1585 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6889 (mm) outliers start: 51 outliers final: 14 residues processed: 202 average time/residue: 1.1957 time to fit residues: 262.2053 Evaluate side-chains 173 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1585 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 413 GLN A 936 GLN A1122 GLN A1268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11062 Z= 0.254 Angle : 0.541 8.386 15001 Z= 0.283 Chirality : 0.040 0.160 1675 Planarity : 0.004 0.047 1848 Dihedral : 9.199 149.590 1584 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.05 % Allowed : 21.47 % Favored : 74.48 % 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: 0.94 (0.24), residues: 1298 helix: 1.45 (0.20), residues: 715 sheet: 0.46 (0.51), residues: 93 loop : -0.52 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 473 HIS 0.005 0.001 HIS A1413 PHE 0.017 0.002 PHE A 894 TYR 0.017 0.002 TYR A 912 ARG 0.003 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 157 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8480 (pt) REVERT: A 280 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7709 (mm110) REVERT: A 728 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: A 902 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7553 (mmp-170) outliers start: 47 outliers final: 20 residues processed: 188 average time/residue: 1.2098 time to fit residues: 246.3330 Evaluate side-chains 178 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 363 GLN A 936 GLN A1058 GLN A1122 GLN A1268 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11062 Z= 0.185 Angle : 0.495 8.855 15001 Z= 0.259 Chirality : 0.038 0.166 1675 Planarity : 0.004 0.042 1848 Dihedral : 9.084 149.234 1584 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.31 % Allowed : 20.86 % Favored : 74.83 % 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: 1.05 (0.24), residues: 1298 helix: 1.56 (0.20), residues: 718 sheet: 0.51 (0.50), residues: 93 loop : -0.53 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.003 0.001 HIS A 742 PHE 0.022 0.001 PHE A1132 TYR 0.014 0.001 TYR A 912 ARG 0.008 0.000 ARG A1427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 156 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8509 (pt) REVERT: A 280 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7522 (mm-40) REVERT: A 461 LYS cc_start: 0.7428 (mptt) cc_final: 0.7213 (mptt) REVERT: A 728 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: A 902 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7528 (mmp-170) REVERT: A 1033 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8329 (mt) REVERT: A 1585 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6897 (mm) outliers start: 50 outliers final: 23 residues processed: 188 average time/residue: 1.2159 time to fit residues: 247.6945 Evaluate side-chains 181 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1434 ASN Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1556 MET Chi-restraints excluded: chain A residue 1585 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 0.0020 chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A1058 GLN A1122 GLN A1268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11062 Z= 0.228 Angle : 0.515 8.107 15001 Z= 0.271 Chirality : 0.039 0.139 1675 Planarity : 0.004 0.043 1848 Dihedral : 9.083 149.005 1584 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.71 % Allowed : 21.98 % Favored : 74.31 % 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: 0.99 (0.23), residues: 1298 helix: 1.52 (0.20), residues: 718 sheet: 0.55 (0.50), residues: 93 loop : -0.58 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 473 HIS 0.004 0.001 HIS A 742 PHE 0.012 0.002 PHE A 585 TYR 0.016 0.002 TYR A 912 ARG 0.005 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8531 (pt) REVERT: A 280 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7571 (mm-40) REVERT: A 728 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: A 902 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7539 (mmp-170) REVERT: A 1033 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8329 (mt) REVERT: A 1585 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6941 (mm) outliers start: 43 outliers final: 23 residues processed: 179 average time/residue: 1.1871 time to fit residues: 230.4822 Evaluate side-chains 180 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1556 MET Chi-restraints excluded: chain A residue 1585 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.4980 chunk 25 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A1058 GLN A1268 ASN A1482 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11062 Z= 0.140 Angle : 0.461 7.479 15001 Z= 0.242 Chirality : 0.037 0.137 1675 Planarity : 0.003 0.039 1848 Dihedral : 8.920 149.551 1584 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.71 % Allowed : 22.16 % Favored : 74.14 % 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: 1.21 (0.24), residues: 1298 helix: 1.73 (0.20), residues: 717 sheet: 0.59 (0.50), residues: 91 loop : -0.52 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.003 0.001 HIS A1413 PHE 0.027 0.001 PHE A1132 TYR 0.012 0.001 TYR A 912 ARG 0.005 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8541 (pt) REVERT: A 303 LYS cc_start: 0.8443 (mptt) cc_final: 0.8239 (mmtt) REVERT: A 728 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: A 902 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7491 (mmp-170) REVERT: A 1107 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8740 (mm) outliers start: 43 outliers final: 21 residues processed: 182 average time/residue: 1.2198 time to fit residues: 240.4182 Evaluate side-chains 174 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1434 ASN Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1556 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 127 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A1058 GLN A1268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11062 Z= 0.167 Angle : 0.479 7.554 15001 Z= 0.251 Chirality : 0.038 0.134 1675 Planarity : 0.003 0.040 1848 Dihedral : 8.881 149.290 1581 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.45 % Allowed : 22.84 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1298 helix: 1.75 (0.20), residues: 717 sheet: 0.66 (0.51), residues: 91 loop : -0.46 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.004 0.001 HIS A1413 PHE 0.011 0.001 PHE A 585 TYR 0.013 0.001 TYR A 352 ARG 0.005 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8545 (pt) REVERT: A 303 LYS cc_start: 0.8425 (mptt) cc_final: 0.8221 (mmtt) REVERT: A 728 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: A 892 ARG cc_start: 0.7942 (mmt-90) cc_final: 0.7707 (mmp80) REVERT: A 902 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7494 (mmp-170) REVERT: A 1107 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8744 (mm) outliers start: 40 outliers final: 26 residues processed: 183 average time/residue: 1.2010 time to fit residues: 238.7265 Evaluate side-chains 178 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1434 ASN Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 936 GLN A1058 GLN A1268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11062 Z= 0.183 Angle : 0.490 7.592 15001 Z= 0.257 Chirality : 0.038 0.136 1675 Planarity : 0.004 0.040 1848 Dihedral : 8.910 149.150 1581 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.36 % Allowed : 23.10 % Favored : 73.53 % 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 (0.24), residues: 1298 helix: 1.70 (0.20), residues: 717 sheet: 0.67 (0.50), residues: 93 loop : -0.45 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.004 0.001 HIS A1413 PHE 0.012 0.001 PHE A 585 TYR 0.013 0.001 TYR A 912 ARG 0.004 0.000 ARG A1405 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8556 (pt) REVERT: A 303 LYS cc_start: 0.8421 (mptt) cc_final: 0.8213 (mmtt) REVERT: A 728 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 892 ARG cc_start: 0.7940 (mmt-90) cc_final: 0.7704 (mmp80) REVERT: A 902 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7502 (mmp-170) REVERT: A 1107 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8753 (mm) REVERT: A 1271 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.6390 (tmm) outliers start: 39 outliers final: 26 residues processed: 175 average time/residue: 1.1382 time to fit residues: 215.9832 Evaluate side-chains 178 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1434 ASN Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.0370 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 76 optimal weight: 0.0970 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A1058 GLN A1268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11062 Z= 0.162 Angle : 0.480 7.479 15001 Z= 0.252 Chirality : 0.038 0.135 1675 Planarity : 0.003 0.039 1848 Dihedral : 8.874 149.098 1581 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.93 % Allowed : 23.71 % Favored : 73.36 % 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: 1.27 (0.24), residues: 1298 helix: 1.73 (0.20), residues: 716 sheet: 0.66 (0.51), residues: 91 loop : -0.40 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.004 0.001 HIS A1413 PHE 0.028 0.001 PHE A1132 TYR 0.012 0.001 TYR A 912 ARG 0.004 0.000 ARG A1405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8550 (pt) REVERT: A 303 LYS cc_start: 0.8399 (mptt) cc_final: 0.8189 (mmtt) REVERT: A 728 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: A 892 ARG cc_start: 0.7949 (mmt-90) cc_final: 0.7706 (mmp80) REVERT: A 902 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7497 (mmp-170) REVERT: A 1107 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8747 (mm) REVERT: A 1271 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6417 (tmm) outliers start: 34 outliers final: 25 residues processed: 175 average time/residue: 1.2029 time to fit residues: 228.1294 Evaluate side-chains 176 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1434 ASN Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1516 GLU Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.0000 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 351 ASN A 592 GLN A 936 GLN A1058 GLN A1268 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11062 Z= 0.192 Angle : 0.495 7.604 15001 Z= 0.260 Chirality : 0.039 0.136 1675 Planarity : 0.004 0.040 1848 Dihedral : 8.916 148.971 1579 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 2.84 % Allowed : 23.79 % Favored : 73.36 % 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: 1.21 (0.24), residues: 1298 helix: 1.67 (0.20), residues: 717 sheet: 0.63 (0.50), residues: 93 loop : -0.41 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.004 0.001 HIS A 742 PHE 0.012 0.001 PHE A 585 TYR 0.013 0.001 TYR A 352 ARG 0.005 0.000 ARG A1405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8531 (pt) REVERT: A 280 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7439 (mm110) REVERT: A 303 LYS cc_start: 0.8423 (mptt) cc_final: 0.8214 (mmtt) REVERT: A 728 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: A 892 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7706 (mmp80) REVERT: A 902 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7511 (mmp-170) REVERT: A 1107 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 1271 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6430 (tmm) outliers start: 33 outliers final: 23 residues processed: 177 average time/residue: 1.1733 time to fit residues: 226.2131 Evaluate side-chains 179 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1516 GLU Chi-restraints excluded: chain A residue 1554 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 75 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 875 GLN A 936 GLN A1058 GLN A1268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.172681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.145700 restraints weight = 11429.789| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.00 r_work: 0.3288 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11062 Z= 0.163 Angle : 0.486 7.496 15001 Z= 0.254 Chirality : 0.038 0.135 1675 Planarity : 0.004 0.039 1848 Dihedral : 8.879 148.975 1579 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.47 % Favored : 97.46 % Rotamer: Outliers : 2.93 % Allowed : 23.71 % Favored : 73.36 % 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: 1.27 (0.24), residues: 1298 helix: 1.72 (0.20), residues: 715 sheet: 0.62 (0.51), residues: 91 loop : -0.37 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.004 0.001 HIS A1413 PHE 0.029 0.001 PHE A1132 TYR 0.012 0.001 TYR A 912 ARG 0.005 0.000 ARG A1405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4421.05 seconds wall clock time: 78 minutes 37.28 seconds (4717.28 seconds total)