Starting phenix.real_space_refine on Wed Jul 30 15:05:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2f_27834/07_2025/8e2f_27834.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2f_27834/07_2025/8e2f_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/cci-nas-00/data/ceres_data/8e2f_27834/07_2025/8e2f_27834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2f_27834/07_2025/8e2f_27834.map" model { file = "/net/cci-nas-00/data/ceres_data/8e2f_27834/07_2025/8e2f_27834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2f_27834/07_2025/8e2f_27834.cif" } 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. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.98, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.44 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: 5.14 Time building geometry restraints manager: 4.04 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: 0.00 - 1.66: 22190 1.66 - 3.33: 281 3.33 - 4.99: 38 4.99 - 6.65: 6 6.65 - 8.32: 1 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: 5188 17.46 - 34.91: 409 34.91 - 52.37: 148 52.37 - 69.83: 49 69.83 - 87.29: 8 Dihedral angle restraints: 5802 sinusoidal: 3198 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 5799 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 2.450 nonbonded pdb=" OD2 ASP A1105 " pdb="HH11 ARG A1304 " model vdw 1.561 2.450 nonbonded pdb=" OE1 GLU A1825 " pdb=" H GLU A1825 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP A1193 " pdb=" H LEU A1194 " model vdw 1.608 2.450 nonbonded pdb=" O SER A1085 " pdb=" HE2 HIS A1089 " model vdw 1.626 2.450 ... (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: 0.000 Normalize map: mean=0, sd=1: 6.750 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: 0.210 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.000 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.070 ------------------------------------------------------------------------------- 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= 0.139 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 % Allowed : 17.84 % Favored : 80.58 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1077 HIS 0.005 0.001 HIS A1784 PHE 0.009 0.001 PHE A1452 TYR 0.008 0.001 TYR A1878 ARG 0.003 0.000 ARG A1406 Details of bonding type rmsd hydrogen bonds : bond 0.10884 ( 337) hydrogen bonds : angle 5.67519 ( 948) covalent geometry : bond 0.00291 ( 6214) covalent geometry : angle 0.61942 ( 8425) *********************** 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 to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 2.0906 time to fit residues: 223.1569 Evaluate side-chains 94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1112 SER Chi-restraints excluded: chain A residue 1127 ASN Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1811 ASP Chi-restraints excluded: chain A residue 2128 SER Chi-restraints excluded: chain A residue 2137 SER Chi-restraints excluded: chain A residue 2330 SER 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: 0.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1051 GLN A1127 ASN A1414 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136068 restraints weight = 21149.146| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.70 r_work: 0.3682 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6214 Z= 0.161 Angle : 0.571 5.864 8425 Z= 0.294 Chirality : 0.039 0.139 1009 Planarity : 0.004 0.035 1052 Dihedral : 5.692 46.133 822 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.16 % Allowed : 16.69 % Favored : 81.15 % 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: 1.03 (0.31), residues: 743 helix: 1.59 (0.27), residues: 369 sheet: 0.12 (0.50), residues: 108 loop : -0.27 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1077 HIS 0.005 0.001 HIS A1784 PHE 0.010 0.001 PHE A1106 TYR 0.011 0.001 TYR A1878 ARG 0.003 0.000 ARG A1304 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 337) hydrogen bonds : angle 4.87117 ( 948) covalent geometry : bond 0.00368 ( 6214) covalent geometry : angle 0.57095 ( 8425) *********************** 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 112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1896 ASP cc_start: 0.7243 (t0) cc_final: 0.7032 (m-30) REVERT: A 2013 ASP cc_start: 0.7217 (m-30) cc_final: 0.6918 (p0) REVERT: A 2084 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7811 (mt0) outliers start: 15 outliers final: 7 residues processed: 107 average time/residue: 2.0237 time to fit residues: 231.0167 Evaluate side-chains 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1364 SER Chi-restraints excluded: chain A residue 1430 LYS Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain A residue 2084 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.0470 chunk 76 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1127 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136342 restraints weight = 21572.961| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.71 r_work: 0.3685 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6214 Z= 0.136 Angle : 0.540 5.812 8425 Z= 0.277 Chirality : 0.038 0.144 1009 Planarity : 0.004 0.033 1052 Dihedral : 4.727 29.842 811 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.45 % Allowed : 16.26 % Favored : 81.29 % 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: 1.11 (0.31), residues: 743 helix: 1.70 (0.27), residues: 371 sheet: 0.11 (0.51), residues: 102 loop : -0.28 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1450 HIS 0.004 0.001 HIS A1089 PHE 0.017 0.001 PHE A1790 TYR 0.010 0.001 TYR A1878 ARG 0.002 0.000 ARG A1406 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 337) hydrogen bonds : angle 4.65478 ( 948) covalent geometry : bond 0.00312 ( 6214) covalent geometry : angle 0.54033 ( 8425) *********************** 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 to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1346 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7141 (pt0) REVERT: A 1511 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: A 2013 ASP cc_start: 0.7226 (m-30) cc_final: 0.6980 (p0) REVERT: A 2084 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7725 (mt0) outliers start: 17 outliers final: 5 residues processed: 108 average time/residue: 2.0134 time to fit residues: 232.0546 Evaluate side-chains 98 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1346 GLU Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2084 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1127 ASN A1414 ASN A1840 HIS ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.157004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136269 restraints weight = 21232.714| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.69 r_work: 0.3687 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6214 Z= 0.140 Angle : 0.537 5.799 8425 Z= 0.274 Chirality : 0.038 0.142 1009 Planarity : 0.004 0.033 1052 Dihedral : 4.690 29.800 811 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.59 % Allowed : 16.26 % Favored : 81.15 % 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: 1.24 (0.31), residues: 743 helix: 1.87 (0.27), residues: 365 sheet: -0.01 (0.51), residues: 104 loop : -0.21 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1077 HIS 0.003 0.001 HIS A1089 PHE 0.009 0.001 PHE A1106 TYR 0.010 0.001 TYR A1878 ARG 0.005 0.000 ARG A1797 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 337) hydrogen bonds : angle 4.52547 ( 948) covalent geometry : bond 0.00321 ( 6214) covalent geometry : angle 0.53664 ( 8425) *********************** 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 to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1194 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8123 (mt) REVERT: A 1346 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: A 1511 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: A 2013 ASP cc_start: 0.7185 (m-30) cc_final: 0.6978 (p0) REVERT: A 2084 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7714 (mt0) outliers start: 18 outliers final: 9 residues processed: 106 average time/residue: 1.9179 time to fit residues: 216.9070 Evaluate side-chains 104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1346 GLU Chi-restraints excluded: chain A residue 1364 SER Chi-restraints excluded: chain A residue 1430 LYS Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1816 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2084 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.157212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136686 restraints weight = 21220.553| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.67 r_work: 0.3689 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1127 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= 0.129 Angle : 0.528 5.775 8425 Z= 0.270 Chirality : 0.038 0.140 1009 Planarity : 0.004 0.033 1052 Dihedral : 4.578 29.632 811 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.88 % Allowed : 16.69 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.32), residues: 743 helix: 1.95 (0.27), residues: 365 sheet: 0.03 (0.51), residues: 104 loop : -0.20 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1077 HIS 0.004 0.001 HIS A1089 PHE 0.018 0.001 PHE A1790 TYR 0.010 0.001 TYR A1878 ARG 0.002 0.000 ARG A1304 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 337) hydrogen bonds : angle 4.42185 ( 948) covalent geometry : bond 0.00297 ( 6214) covalent geometry : angle 0.52764 ( 8425) *********************** 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 to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1194 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8127 (mt) REVERT: A 1346 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7144 (pt0) REVERT: A 1511 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: A 2084 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7643 (mt0) REVERT: A 2577 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8054 (tt0) outliers start: 20 outliers final: 7 residues processed: 105 average time/residue: 2.3253 time to fit residues: 260.2762 Evaluate side-chains 100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1346 GLU Chi-restraints excluded: chain A residue 1430 LYS Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1816 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2577 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136360 restraints weight = 21570.772| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.68 r_work: 0.3692 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6214 Z= 0.134 Angle : 0.529 5.798 8425 Z= 0.270 Chirality : 0.038 0.140 1009 Planarity : 0.004 0.048 1052 Dihedral : 4.545 29.604 811 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.02 % Allowed : 16.55 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.32), residues: 743 helix: 1.95 (0.27), residues: 365 sheet: 0.03 (0.51), residues: 104 loop : -0.19 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1077 HIS 0.004 0.001 HIS A1089 PHE 0.009 0.001 PHE A1452 TYR 0.010 0.001 TYR A1878 ARG 0.003 0.000 ARG A1304 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 337) hydrogen bonds : angle 4.39044 ( 948) covalent geometry : bond 0.00309 ( 6214) covalent geometry : angle 0.52872 ( 8425) *********************** 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 to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1194 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8156 (mt) REVERT: A 1346 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: A 1511 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: A 2084 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: A 2577 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8061 (tt0) outliers start: 21 outliers final: 9 residues processed: 107 average time/residue: 2.7134 time to fit residues: 310.6145 Evaluate side-chains 104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1346 GLU Chi-restraints excluded: chain A residue 1364 SER Chi-restraints excluded: chain A residue 1430 LYS Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1816 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2577 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135018 restraints weight = 21402.472| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.67 r_work: 0.3672 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6214 Z= 0.167 Angle : 0.553 5.980 8425 Z= 0.282 Chirality : 0.039 0.155 1009 Planarity : 0.004 0.052 1052 Dihedral : 4.636 29.885 811 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.73 % Allowed : 17.12 % Favored : 80.14 % 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: 1.25 (0.32), residues: 743 helix: 1.88 (0.27), residues: 363 sheet: 0.05 (0.51), residues: 104 loop : -0.21 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1077 HIS 0.004 0.001 HIS A1895 PHE 0.020 0.002 PHE A1790 TYR 0.012 0.001 TYR A1878 ARG 0.010 0.001 ARG A2360 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 337) hydrogen bonds : angle 4.41828 ( 948) covalent geometry : bond 0.00387 ( 6214) covalent geometry : angle 0.55251 ( 8425) *********************** 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 111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1194 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8164 (mt) REVERT: A 1346 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7156 (pt0) REVERT: A 1511 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: A 2084 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: A 2326 GLU cc_start: 0.6505 (pm20) cc_final: 0.5973 (pm20) REVERT: A 2577 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8082 (tt0) outliers start: 19 outliers final: 10 residues processed: 107 average time/residue: 2.1144 time to fit residues: 241.1507 Evaluate side-chains 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1346 GLU Chi-restraints excluded: chain A residue 1364 SER Chi-restraints excluded: chain A residue 1430 LYS Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1816 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2577 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.156206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135533 restraints weight = 21628.172| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.69 r_work: 0.3678 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: 0.8244 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6214 Z= 0.145 Angle : 0.543 5.857 8425 Z= 0.276 Chirality : 0.038 0.147 1009 Planarity : 0.004 0.035 1052 Dihedral : 4.606 29.961 811 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.59 % Allowed : 17.70 % Favored : 79.71 % 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: 1.29 (0.31), residues: 743 helix: 1.91 (0.27), residues: 363 sheet: 0.10 (0.51), residues: 103 loop : -0.19 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1077 HIS 0.004 0.001 HIS A1089 PHE 0.010 0.001 PHE A1452 TYR 0.011 0.001 TYR A1878 ARG 0.003 0.000 ARG A2360 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 337) hydrogen bonds : angle 4.37529 ( 948) covalent geometry : bond 0.00335 ( 6214) covalent geometry : angle 0.54319 ( 8425) *********************** 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 105 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1194 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8163 (mt) REVERT: A 1346 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7159 (pt0) REVERT: A 1511 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: A 2084 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: A 2577 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8074 (tt0) outliers start: 18 outliers final: 10 residues processed: 100 average time/residue: 2.1633 time to fit residues: 230.2024 Evaluate side-chains 100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1113 ASN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1346 GLU Chi-restraints excluded: chain A residue 1364 SER Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1816 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2137 SER Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2577 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 70 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.156655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136084 restraints weight = 21399.204| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.68 r_work: 0.3681 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6214 Z= 0.133 Angle : 0.547 6.537 8425 Z= 0.279 Chirality : 0.038 0.152 1009 Planarity : 0.004 0.033 1052 Dihedral : 4.561 29.999 811 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.45 % Allowed : 17.84 % Favored : 79.71 % 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: 1.34 (0.32), residues: 743 helix: 1.96 (0.27), residues: 363 sheet: 0.11 (0.51), residues: 103 loop : -0.19 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1077 HIS 0.003 0.001 HIS A1089 PHE 0.010 0.001 PHE A1452 TYR 0.010 0.001 TYR A1878 ARG 0.004 0.000 ARG A2360 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 337) hydrogen bonds : angle 4.35265 ( 948) covalent geometry : bond 0.00306 ( 6214) covalent geometry : angle 0.54703 ( 8425) *********************** 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 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1194 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8148 (mt) REVERT: A 1346 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7164 (pt0) REVERT: A 2084 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: A 2326 GLU cc_start: 0.6594 (pm20) cc_final: 0.5993 (pm20) REVERT: A 2577 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8063 (tt0) outliers start: 17 outliers final: 8 residues processed: 97 average time/residue: 2.8244 time to fit residues: 293.5653 Evaluate side-chains 97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1346 GLU Chi-restraints excluded: chain A residue 1364 SER Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1816 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2084 GLN Chi-restraints excluded: chain A residue 2137 SER Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2577 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4002 r_free = 0.4002 target = 0.157369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136939 restraints weight = 21282.995| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.66 r_work: 0.3693 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6214 Z= 0.125 Angle : 0.535 6.495 8425 Z= 0.271 Chirality : 0.038 0.150 1009 Planarity : 0.004 0.034 1052 Dihedral : 4.495 30.059 811 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.16 % Allowed : 17.84 % Favored : 80.00 % 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: 1.39 (0.32), residues: 743 helix: 2.00 (0.27), residues: 363 sheet: 0.13 (0.51), residues: 103 loop : -0.16 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1077 HIS 0.003 0.001 HIS A1223 PHE 0.023 0.001 PHE A1790 TYR 0.009 0.001 TYR A1878 ARG 0.004 0.000 ARG A2360 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 337) hydrogen bonds : angle 4.30807 ( 948) covalent geometry : bond 0.00289 ( 6214) covalent geometry : angle 0.53463 ( 8425) ********************** 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 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1126 LYS cc_start: 0.6405 (mmtt) cc_final: 0.6041 (mtmt) REVERT: A 1194 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8155 (mt) REVERT: A 1346 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7157 (pt0) REVERT: A 2326 GLU cc_start: 0.6666 (pm20) cc_final: 0.6039 (pm20) REVERT: A 2577 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8046 (tt0) outliers start: 15 outliers final: 10 residues processed: 98 average time/residue: 2.0731 time to fit residues: 216.0803 Evaluate side-chains 97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1346 GLU Chi-restraints excluded: chain A residue 1364 SER Chi-restraints excluded: chain A residue 1430 LYS Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1816 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 2137 SER Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2577 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 3 optimal weight: 0.0370 chunk 52 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.158196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137759 restraints weight = 21344.590| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.67 r_work: 0.3704 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1524 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= 0.113 Angle : 0.523 7.004 8425 Z= 0.265 Chirality : 0.038 0.149 1009 Planarity : 0.004 0.033 1052 Dihedral : 4.403 30.006 811 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.87 % Allowed : 18.56 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.32), residues: 743 helix: 2.11 (0.27), residues: 363 sheet: 0.16 (0.51), residues: 103 loop : -0.12 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1077 HIS 0.003 0.001 HIS A1223 PHE 0.008 0.001 PHE A1106 TYR 0.007 0.001 TYR A1878 ARG 0.004 0.000 ARG A2360 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 337) hydrogen bonds : angle 4.25761 ( 948) covalent geometry : bond 0.00262 ( 6214) covalent geometry : angle 0.52330 ( 8425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10026.78 seconds wall clock time: 177 minutes 35.72 seconds (10655.72 seconds total)