Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 17:44:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2f_27834/08_2023/8e2f_27834.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2f_27834/08_2023/8e2f_27834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2f_27834/08_2023/8e2f_27834.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2f_27834/08_2023/8e2f_27834.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2f_27834/08_2023/8e2f_27834.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2f_27834/08_2023/8e2f_27834.pdb" } resolution = 2.47 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= -0.004 sd= 0.080 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 S 40 5.16 5 C 3905 2.51 5 N 1046 2.21 5 O 1107 1.98 5 H 6207 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1052": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1175": "OE1" <-> "OE2" Residue "A GLU 1179": "OE1" <-> "OE2" Residue "A ASP 1180": "OD1" <-> "OD2" Residue "A GLU 1298": "OE1" <-> "OE2" Residue "A PHE 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1395": "OE1" <-> "OE2" Residue "A TYR 1499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1511": "OE1" <-> "OE2" Residue "A GLU 1562": "OE1" <-> "OE2" Residue "A ASP 1803": "OD1" <-> "OD2" Residue "A ASP 1818": "OD1" <-> "OD2" Residue "A GLU 1825": "OE1" <-> "OE2" Residue "A ASP 1827": "OD1" <-> "OD2" Residue "A PHE 1877": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1888": "OE1" <-> "OE2" Residue "A ASP 1896": "OD1" <-> "OD2" Residue "A GLU 2089": "OE1" <-> "OE2" Residue "A ASP 2143": "OD1" <-> "OD2" Residue "A TYR 2181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2576": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 12305 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 12305 Classifications: {'peptide': 771} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 13 Time building chain proxies: 5.42, per 1000 atoms: 0.44 Number of scatterers: 12305 At special positions: 0 Unit cell: (82.72, 84.48, 115.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 1107 8.00 N 1046 7.00 C 3905 6.00 H 6207 1.00 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: 10.37 Conformation dependent library (CDL) restraints added in 943.6 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 52.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 1018 through 1028 Processing helix chain 'A' and resid 1050 through 1055 Processing helix chain 'A' and resid 1060 through 1067 removed outlier: 4.424A pdb=" N GLN A1065 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1171 through 1177 Processing helix chain 'A' and resid 1189 through 1192 Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1291 through 1294 Processing helix chain 'A' and resid 1313 through 1324 Processing helix chain 'A' and resid 1324 through 1336 removed outlier: 3.614A pdb=" N HIS A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1343 Processing helix chain 'A' and resid 1345 through 1364 Processing helix chain 'A' and resid 1377 through 1384 Processing helix chain 'A' and resid 1384 through 1395 removed outlier: 3.559A pdb=" N GLU A1395 " --> pdb=" O VAL A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1414 Processing helix chain 'A' and resid 1423 through 1436 removed outlier: 4.211A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 Proline residue: A1440 - end of helix No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1444 through 1459 removed outlier: 3.614A pdb=" N TRP A1450 " --> pdb=" O GLY A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1484 removed outlier: 3.624A pdb=" N ARG A1479 " --> pdb=" O THR A1475 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN A1480 " --> pdb=" O ALA A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1496 Processing helix chain 'A' and resid 1823 through 1828 Processing helix chain 'A' and resid 2012 through 2018 Processing helix chain 'A' and resid 2019 through 2041 Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2071 through 2087 Processing helix chain 'A' and resid 2091 through 2105 Processing helix chain 'A' and resid 2113 through 2128 Processing helix chain 'A' and resid 2132 through 2147 removed outlier: 3.546A pdb=" N GLU A2136 " --> pdb=" O SER A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2150 No H-bonds generated for 'chain 'A' and resid 2148 through 2150' Processing helix chain 'A' and resid 2164 through 2182 Processing helix chain 'A' and resid 2326 through 2341 Processing helix chain 'A' and resid 2348 through 2365 removed outlier: 3.570A pdb=" N LEU A2352 " --> pdb=" O ALA A2348 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A2353 " --> pdb=" O ASP A2349 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A2365 " --> pdb=" O ILE A2361 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2574 removed outlier: 3.565A pdb=" N GLU A2572 " --> pdb=" O ALA A2569 " (cutoff:3.500A) Processing helix chain 'A' and resid 2576 through 2599 Processing sheet with id=AA1, first strand: chain 'A' and resid 1031 through 1033 removed outlier: 6.504A pdb=" N GLN A1297 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1031 through 1033 removed outlier: 5.450A pdb=" N PHE A1306 " --> pdb=" O VAL A1101 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A1101 " --> pdb=" O PHE A1306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 6.621A pdb=" N ILE A1120 " --> pdb=" O VAL A1186 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A1186 " --> pdb=" O ILE A1120 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A1122 " --> pdb=" O GLY A1184 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY A1184 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A1124 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1564 through 1565 removed outlier: 6.679A pdb=" N HIS A1881 " --> pdb=" O LEU A1801 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU A1801 " --> pdb=" O HIS A1881 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ARG A1854 " --> pdb=" O PHE A1795 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N ARG A1797 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N VAL A1852 " --> pdb=" O ARG A1797 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE A1855 " --> pdb=" O ILE A1819 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE A1819 " --> pdb=" O PHE A1855 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A1857 " --> pdb=" O ILE A1817 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A1817 " --> pdb=" O LYS A1857 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR A1859 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A1815 " --> pdb=" O THR A1859 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A1861 " --> pdb=" O ALA A1813 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A1815 " --> pdb=" O VAL A1833 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL A1833 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A1817 " --> pdb=" O LEU A1831 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1569 through 1573 removed outlier: 6.795A pdb=" N THR A1792 " --> pdb=" O VAL A1571 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR A1573 " --> pdb=" O PHE A1790 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A1790 " --> pdb=" O THR A1573 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1578 through 1580 339 hydrogen bonds defined for protein. 948 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: 4.85 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6184 1.03 - 1.23: 29 1.23 - 1.42: 2497 1.42 - 1.62: 3654 1.62 - 1.81: 57 Bond restraints: 12421 Sorted by residual: bond pdb=" CB GLN A2057 " pdb=" CG GLN A2057 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" N VAL A1506 " pdb=" CA VAL A1506 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.15e-02 7.56e+03 1.21e+00 bond pdb=" N GLY A1880 " pdb=" CA GLY A1880 " ideal model delta sigma weight residual 1.455 1.443 0.011 1.05e-02 9.07e+03 1.18e+00 bond pdb=" CB GLU A2326 " pdb=" CG GLU A2326 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" CB PRO A1036 " pdb=" CG PRO A1036 " ideal model delta sigma weight residual 1.492 1.543 -0.051 5.00e-02 4.00e+02 1.02e+00 ... (remaining 12416 not shown) Histogram of bond angle deviations from ideal: 100.25 - 106.99: 303 106.99 - 113.73: 15110 113.73 - 120.48: 3797 120.48 - 127.22: 3224 127.22 - 133.97: 82 Bond angle restraints: 22516 Sorted by residual: angle pdb=" N GLN A2051 " pdb=" CA GLN A2051 " pdb=" C GLN A2051 " ideal model delta sigma weight residual 113.55 108.58 4.97 1.26e+00 6.30e-01 1.55e+01 angle pdb=" CB MET A1783 " pdb=" CG MET A1783 " pdb=" SD MET A1783 " ideal model delta sigma weight residual 112.70 121.02 -8.32 3.00e+00 1.11e-01 7.69e+00 angle pdb=" CA GLN A2057 " pdb=" CB GLN A2057 " pdb=" CG GLN A2057 " ideal model delta sigma weight residual 114.10 119.63 -5.53 2.00e+00 2.50e-01 7.65e+00 angle pdb=" C ALA A1198 " pdb=" N GLY A1199 " pdb=" CA GLY A1199 " ideal model delta sigma weight residual 121.83 118.42 3.41 1.30e+00 5.92e-01 6.88e+00 angle pdb=" N ALA A1198 " pdb=" CA ALA A1198 " pdb=" C ALA A1198 " ideal model delta sigma weight residual 110.80 106.04 4.76 2.13e+00 2.20e-01 5.00e+00 ... (remaining 22511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4480 17.46 - 34.91: 363 34.91 - 52.37: 99 52.37 - 69.83: 29 69.83 - 87.29: 8 Dihedral angle restraints: 4979 sinusoidal: 2375 harmonic: 2604 Sorted by residual: dihedral pdb=" CA GLN A1323 " pdb=" C GLN A1323 " pdb=" N PHE A1324 " pdb=" CA PHE A1324 " ideal model delta harmonic sigma weight residual -180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ILE A1848 " pdb=" C ILE A1848 " pdb=" N PRO A1849 " pdb=" CA PRO A1849 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ALA A2048 " pdb=" C ALA A2048 " pdb=" N VAL A2049 " pdb=" CA VAL A2049 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 4976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 699 0.032 - 0.065: 215 0.065 - 0.097: 63 0.097 - 0.129: 27 0.129 - 0.161: 5 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA ILE A1858 " pdb=" N ILE A1858 " pdb=" C ILE A1858 " pdb=" CB ILE A1858 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE A1873 " pdb=" N ILE A1873 " pdb=" C ILE A1873 " pdb=" CB ILE A1873 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE A1780 " pdb=" N ILE A1780 " pdb=" C ILE A1780 " pdb=" CB ILE A1780 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1006 not shown) Planarity restraints: 1775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A1113 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ASN A1113 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN A1113 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A1114 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1385 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LEU A1385 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU A1385 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A1386 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A1425 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A1426 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A1426 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1426 " -0.017 5.00e-02 4.00e+02 ... (remaining 1772 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 159 2.05 - 2.69: 19554 2.69 - 3.32: 38110 3.32 - 3.96: 49726 3.96 - 4.60: 77291 Nonbonded interactions: 184840 Sorted by model distance: nonbonded pdb=" OE1 GLU A2326 " pdb=" H GLU A2326 " model vdw 1.409 1.850 nonbonded pdb=" OD2 ASP A1105 " pdb="HH11 ARG A1304 " model vdw 1.561 1.850 nonbonded pdb=" OE1 GLU A1825 " pdb=" H GLU A1825 " model vdw 1.577 1.850 nonbonded pdb=" OD1 ASP A1193 " pdb=" H LEU A1194 " model vdw 1.608 1.850 nonbonded pdb=" O SER A1085 " pdb=" HE2 HIS A1089 " model vdw 1.626 1.850 ... (remaining 184835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.370 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: 0.180 Extract box with map and model: 24.210 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 42.060 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 0.051 6214 Z= 0.196 Angle : 0.619 8.319 8425 Z= 0.337 Chirality : 0.038 0.161 1009 Planarity : 0.004 0.031 1052 Dihedral : 16.352 87.285 2279 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.58 % 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 (0.32), residues: 743 helix: 1.61 (0.27), residues: 368 sheet: 0.10 (0.49), residues: 108 loop : -0.23 (0.40), residues: 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 2.0471 time to fit residues: 217.8900 Evaluate side-chains 94 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.2779 time to fit residues: 1.5708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1051 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 6214 Z= 0.231 Angle : 0.557 5.966 8425 Z= 0.284 Chirality : 0.039 0.143 1009 Planarity : 0.004 0.030 1052 Dihedral : 4.702 18.292 810 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 3.02 % 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: 1.16 (0.32), residues: 743 helix: 1.66 (0.27), residues: 369 sheet: 0.25 (0.50), residues: 108 loop : -0.18 (0.41), residues: 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 109 average time/residue: 2.0376 time to fit residues: 236.6461 Evaluate side-chains 98 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 1.8571 time to fit residues: 7.1485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 HIS ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6214 Z= 0.262 Angle : 0.564 6.018 8425 Z= 0.288 Chirality : 0.039 0.143 1009 Planarity : 0.004 0.037 1052 Dihedral : 4.743 19.067 810 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 3.31 % 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: 1.28 (0.32), residues: 743 helix: 1.79 (0.27), residues: 365 sheet: 0.18 (0.49), residues: 109 loop : -0.07 (0.41), residues: 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 108 average time/residue: 2.2162 time to fit residues: 254.0598 Evaluate side-chains 102 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.2087 time to fit residues: 1.8665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 6214 Z= 0.213 Angle : 0.537 5.960 8425 Z= 0.273 Chirality : 0.038 0.142 1009 Planarity : 0.003 0.029 1052 Dihedral : 4.623 18.497 810 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 3.02 % 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: 1.40 (0.32), residues: 743 helix: 1.93 (0.27), residues: 365 sheet: 0.20 (0.50), residues: 109 loop : -0.07 (0.41), residues: 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 106 average time/residue: 2.0413 time to fit residues: 230.3933 Evaluate side-chains 104 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.2162 time to fit residues: 1.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6214 Z= 0.252 Angle : 0.550 6.017 8425 Z= 0.281 Chirality : 0.039 0.142 1009 Planarity : 0.004 0.032 1052 Dihedral : 4.671 19.082 810 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 3.17 % 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: 1.34 (0.32), residues: 743 helix: 1.86 (0.27), residues: 363 sheet: 0.28 (0.51), residues: 103 loop : -0.11 (0.39), residues: 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 108 average time/residue: 2.1729 time to fit residues: 248.9315 Evaluate side-chains 104 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.2138 time to fit residues: 1.8806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 6214 Z= 0.179 Angle : 0.529 5.920 8425 Z= 0.267 Chirality : 0.038 0.141 1009 Planarity : 0.004 0.049 1052 Dihedral : 4.494 19.086 810 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 3.02 % 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: 1.54 (0.32), residues: 743 helix: 2.03 (0.27), residues: 363 sheet: 0.30 (0.50), residues: 109 loop : 0.02 (0.40), residues: 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 106 average time/residue: 2.1003 time to fit residues: 237.0718 Evaluate side-chains 95 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.2320 time to fit residues: 2.0545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 6214 Z= 0.229 Angle : 0.536 5.989 8425 Z= 0.272 Chirality : 0.038 0.139 1009 Planarity : 0.004 0.029 1052 Dihedral : 4.504 18.302 810 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 2.73 % 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: 1.52 (0.32), residues: 743 helix: 2.05 (0.27), residues: 363 sheet: 0.17 (0.52), residues: 101 loop : 0.03 (0.39), residues: 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 100 average time/residue: 2.1032 time to fit residues: 224.0003 Evaluate side-chains 99 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.3185 time to fit residues: 2.7162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.0060 chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 6214 Z= 0.184 Angle : 0.521 5.945 8425 Z= 0.263 Chirality : 0.037 0.139 1009 Planarity : 0.004 0.035 1052 Dihedral : 4.397 18.739 810 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 2.30 % 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: 1.60 (0.32), residues: 743 helix: 2.13 (0.27), residues: 363 sheet: 0.16 (0.51), residues: 102 loop : 0.05 (0.39), residues: 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 2.0954 time to fit residues: 214.1595 Evaluate side-chains 93 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.2856 time to fit residues: 1.6656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1840 HIS ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6214 Z= 0.250 Angle : 0.554 6.651 8425 Z= 0.280 Chirality : 0.038 0.137 1009 Planarity : 0.004 0.031 1052 Dihedral : 4.518 18.921 810 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 2.16 % 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: 1.56 (0.32), residues: 743 helix: 2.02 (0.27), residues: 363 sheet: 0.52 (0.52), residues: 100 loop : -0.01 (0.39), residues: 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 96 average time/residue: 2.0544 time to fit residues: 211.9892 Evaluate side-chains 98 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.2245 time to fit residues: 2.4085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.0770 chunk 48 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 6214 Z= 0.171 Angle : 0.525 7.009 8425 Z= 0.264 Chirality : 0.038 0.139 1009 Planarity : 0.003 0.034 1052 Dihedral : 4.368 18.337 810 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.32), residues: 743 helix: 2.18 (0.27), residues: 363 sheet: 0.30 (0.52), residues: 100 loop : 0.12 (0.39), residues: 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 1.9984 time to fit residues: 211.2718 Evaluate side-chains 94 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.3220 time to fit residues: 2.2612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135026 restraints weight = 21273.169| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.69 r_work: 0.3677 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 6214 Z= 0.232 Angle : 0.550 7.146 8425 Z= 0.276 Chirality : 0.038 0.137 1009 Planarity : 0.004 0.032 1052 Dihedral : 4.446 18.049 810 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 1.73 % 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: 1.69 (0.32), residues: 743 helix: 2.11 (0.27), residues: 363 sheet: 0.54 (0.51), residues: 106 loop : 0.08 (0.40), residues: 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5525.02 seconds wall clock time: 97 minutes 36.45 seconds (5856.45 seconds total)