Starting phenix.real_space_refine on Tue Aug 4 22:44:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11lt_75818/08_2026/11lt_75818.cif Found real_map, /net/cci-nas-00/data/ceres_data/11lt_75818/08_2026/11lt_75818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11lt_75818/08_2026/11lt_75818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11lt_75818/08_2026/11lt_75818.map" model { file = "/net/cci-nas-00/data/ceres_data/11lt_75818/08_2026/11lt_75818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11lt_75818/08_2026/11lt_75818.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4466 2.51 5 N 1192 2.21 5 O 1304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7004 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1815 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 14, 'TRANS': 214} Chain: "B" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1519 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 13, 'TRANS': 178} Chain breaks: 1 Chain: "C" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1856 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 1 Chain: "H" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 983 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 831 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Time building chain proxies: 1.39, per 1000 atoms: 0.20 Number of scatterers: 7004 At special positions: 0 Unit cell: (97.11, 104.58, 85.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1304 8.00 N 1192 7.00 C 4466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 341.1 milliseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 17 sheets defined 9.6% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.664A pdb=" N TRP A 163 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 168 through 173 removed outlier: 4.333A pdb=" N THR B 171 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 removed outlier: 3.723A pdb=" N VAL C 47 " --> pdb=" O MET C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.779A pdb=" N GLU C 65 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 66 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 68 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.938A pdb=" N LEU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.097A pdb=" N TYR C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.503A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 76 removed outlier: 5.491A pdb=" N LEU A 68 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET A 241 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 70 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 233 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA C 22 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.841A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA A 248 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.709A pdb=" N VAL B 226 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 154 removed outlier: 6.239A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.472A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 170 through 171 removed outlier: 6.150A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.520A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.589A pdb=" N CYS H 97 " --> pdb=" O TRP H 113 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TRP H 113 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG H 99 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'L' and resid 18 through 21 Processing sheet with id=AB8, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.536A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP L 87 " --> pdb=" O HIS L 40 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR L 98 " --> pdb=" O ARG L 94 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 549 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: 1.08 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2180 1.34 - 1.46: 1809 1.46 - 1.58: 3142 1.58 - 1.71: 0 1.71 - 1.83: 66 Bond restraints: 7197 Sorted by residual: bond pdb=" C ALA A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.65e+00 bond pdb=" CB ASN C 188 " pdb=" CG ASN C 188 " ideal model delta sigma weight residual 1.516 1.575 -0.059 2.50e-02 1.60e+03 5.49e+00 bond pdb=" C LEU A 257 " pdb=" N PRO A 258 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.33e-02 5.65e+03 5.22e+00 bond pdb=" CB ASP C 76 " pdb=" CG ASP C 76 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.69e+00 bond pdb=" CB GLN H 1 " pdb=" CG GLN H 1 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 4.07e+00 ... (remaining 7192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 9656 3.63 - 7.27: 119 7.27 - 10.90: 31 10.90 - 14.54: 1 14.54 - 18.17: 5 Bond angle restraints: 9812 Sorted by residual: angle pdb=" CB MET B 222 " pdb=" CG MET B 222 " pdb=" SD MET B 222 " ideal model delta sigma weight residual 112.70 130.87 -18.17 3.00e+00 1.11e-01 3.67e+01 angle pdb=" CB MET B 193 " pdb=" CG MET B 193 " pdb=" SD MET B 193 " ideal model delta sigma weight residual 112.70 129.80 -17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" CB MET C 148 " pdb=" CG MET C 148 " pdb=" SD MET C 148 " ideal model delta sigma weight residual 112.70 128.22 -15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" CB GLN H 1 " pdb=" CG GLN H 1 " pdb=" CD GLN H 1 " ideal model delta sigma weight residual 112.60 120.57 -7.97 1.70e+00 3.46e-01 2.20e+01 angle pdb=" C MET B 235 " pdb=" N CYS B 236 " pdb=" CA CYS B 236 " ideal model delta sigma weight residual 121.54 130.31 -8.77 1.91e+00 2.74e-01 2.11e+01 ... (remaining 9807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 3606 17.18 - 34.36: 449 34.36 - 51.54: 120 51.54 - 68.73: 22 68.73 - 85.91: 6 Dihedral angle restraints: 4203 sinusoidal: 1623 harmonic: 2580 Sorted by residual: dihedral pdb=" CA LEU A 257 " pdb=" C LEU A 257 " pdb=" N PRO A 258 " pdb=" CA PRO A 258 " ideal model delta harmonic sigma weight residual -180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY B 105 " pdb=" C GLY B 105 " pdb=" N PHE B 106 " pdb=" CA PHE B 106 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA PRO A 258 " pdb=" C PRO A 258 " pdb=" N TYR A 259 " pdb=" CA TYR A 259 " ideal model delta harmonic sigma weight residual 180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 4200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 747 0.047 - 0.094: 226 0.094 - 0.141: 85 0.141 - 0.188: 15 0.188 - 0.236: 10 Chirality restraints: 1083 Sorted by residual: chirality pdb=" CB VAL A 239 " pdb=" CA VAL A 239 " pdb=" CG1 VAL A 239 " pdb=" CG2 VAL A 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ASP C 76 " pdb=" N ASP C 76 " pdb=" C ASP C 76 " pdb=" CB ASP C 76 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE C 153 " pdb=" CA ILE C 153 " pdb=" CG1 ILE C 153 " pdb=" CG2 ILE C 153 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1080 not shown) Planarity restraints: 1257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 37 " -0.024 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP L 37 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP L 37 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP L 37 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 37 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 37 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP L 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 37 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP L 37 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 188 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C ASN C 188 " -0.062 2.00e-02 2.50e+03 pdb=" O ASN C 188 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 189 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 83 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ASN C 83 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN C 83 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE C 84 " -0.020 2.00e-02 2.50e+03 ... (remaining 1254 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1959 2.81 - 3.33: 5638 3.33 - 3.85: 11983 3.85 - 4.38: 13896 4.38 - 4.90: 23891 Nonbonded interactions: 57367 Sorted by model distance: nonbonded pdb=" OH TYR A 76 " pdb=" O ASN A 226 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR B 171 " pdb=" O GLU C 50 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 159 " pdb=" OE2 GLU C 54 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASP A 198 " pdb=" OH TYR A 209 " model vdw 2.325 3.040 nonbonded pdb=" O TYR H 51 " pdb=" OG1 THR H 59 " model vdw 2.353 3.040 ... (remaining 57362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 22.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 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 : 0.005 0.073 7199 Z= 0.229 Angle : 1.098 18.171 9816 Z= 0.558 Chirality : 0.056 0.236 1083 Planarity : 0.008 0.084 1257 Dihedral : 16.619 85.908 2543 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.61 % Allowed : 31.03 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.26), residues: 881 helix: -3.54 (0.44), residues: 57 sheet: -0.22 (0.30), residues: 289 loop : -1.68 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 118 TYR 0.023 0.002 TYR B 64 PHE 0.021 0.002 PHE C 82 TRP 0.060 0.002 TRP L 37 HIS 0.003 0.001 HIS C 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 ( 7197) covalent geometry : angle 1.09815 / 0.56 ( 9812) SS BOND : bond 0.00126 / 0.06 ( 2) SS BOND : angle 1.08967 / 0.53 ( 4) hydrogen bonds : bond 0.16362 / 9.97 ( 201) hydrogen bonds : angle 6.96033 / 4.71 ( 549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.7586 (pp20) cc_final: 0.7264 (tm-30) REVERT: A 229 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7993 (mm110) REVERT: B 111 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8913 (mm-40) REVERT: B 225 MET cc_start: 0.6839 (mtm) cc_final: 0.5881 (pmm) REVERT: C 79 GLN cc_start: 0.8985 (tt0) cc_final: 0.8752 (pt0) REVERT: L 16 GLN cc_start: 0.8503 (pm20) cc_final: 0.8201 (pm20) REVERT: L 28 ASP cc_start: 0.8947 (t0) cc_final: 0.8717 (OUTLIER) REVERT: L 94 ARG cc_start: 0.8885 (ptm-80) cc_final: 0.8468 (ptm-80) outliers start: 20 outliers final: 17 residues processed: 160 average time/residue: 0.5360 time to fit residues: 90.4667 Evaluate side-chains 154 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS H 40 GLN H 60 ASN L 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.082964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.056926 restraints weight = 14752.521| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.14 r_work: 0.2628 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7199 Z= 0.177 Angle : 0.628 9.634 9816 Z= 0.319 Chirality : 0.044 0.153 1083 Planarity : 0.005 0.050 1257 Dihedral : 6.389 57.516 986 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.36 % Favored : 93.53 % Rotamer: Outliers : 5.35 % Allowed : 25.42 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.27), residues: 881 helix: -2.35 (0.64), residues: 53 sheet: -0.16 (0.30), residues: 295 loop : -1.37 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 118 TYR 0.010 0.001 TYR L 51 PHE 0.014 0.001 PHE H 80 TRP 0.022 0.001 TRP L 37 HIS 0.005 0.001 HIS H 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 7197) covalent geometry : angle 0.62778 / 0.32 ( 9812) SS BOND : bond 0.00503 / 0.24 ( 2) SS BOND : angle 0.65121 / 0.37 ( 4) hydrogen bonds : bond 0.03746 / 2.36 ( 201) hydrogen bonds : angle 5.60718 / 3.82 ( 549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.239 Fit side-chains REVERT: A 56 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8142 (tp30) REVERT: A 229 GLN cc_start: 0.8573 (mm-40) cc_final: 0.7979 (mm110) REVERT: B 203 ARG cc_start: 0.8731 (mmt180) cc_final: 0.8168 (mmt180) REVERT: B 225 MET cc_start: 0.6905 (mtm) cc_final: 0.6207 (pmm) REVERT: C 50 GLU cc_start: 0.8868 (pm20) cc_final: 0.8608 (pm20) REVERT: C 171 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7755 (p) REVERT: H 9 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8434 (tp30) REVERT: H 13 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8152 (mmmt) REVERT: H 40 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.9046 (tt0) REVERT: H 74 ASP cc_start: 0.8431 (t0) cc_final: 0.8141 (t0) REVERT: L 55 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8870 (mp0) REVERT: L 81 GLN cc_start: 0.8208 (mm110) cc_final: 0.7991 (mm110) REVERT: L 85 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7732 (mp0) REVERT: L 94 ARG cc_start: 0.9186 (ptm-80) cc_final: 0.8868 (ptm-80) outliers start: 41 outliers final: 25 residues processed: 169 average time/residue: 0.4379 time to fit residues: 78.0527 Evaluate side-chains 159 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 69 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 20 optimal weight: 0.0170 chunk 22 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 overall best weight: 3.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS C 188 ASN C 247 GLN H 40 GLN ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.055506 restraints weight = 14778.294| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.11 r_work: 0.2600 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7199 Z= 0.197 Angle : 0.635 9.805 9816 Z= 0.319 Chirality : 0.045 0.151 1083 Planarity : 0.005 0.048 1257 Dihedral : 6.029 59.377 974 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.62 % Rotamer: Outliers : 5.61 % Allowed : 24.77 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.27), residues: 881 helix: -1.94 (0.67), residues: 53 sheet: -0.05 (0.29), residues: 298 loop : -1.26 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 118 TYR 0.011 0.001 TYR A 76 PHE 0.014 0.001 PHE H 80 TRP 0.010 0.001 TRP L 37 HIS 0.006 0.001 HIS H 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 7197) covalent geometry : angle 0.63523 / 0.32 ( 9812) SS BOND : bond 0.00339 / 0.16 ( 2) SS BOND : angle 0.27466 / 0.16 ( 4) hydrogen bonds : bond 0.03483 / 2.21 ( 201) hydrogen bonds : angle 5.36533 / 3.66 ( 549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.181 Fit side-chains REVERT: A 56 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: A 227 GLU cc_start: 0.7497 (pp20) cc_final: 0.7085 (pp20) REVERT: A 229 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8013 (mm110) REVERT: B 116 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.8885 (mptm) REVERT: C 50 GLU cc_start: 0.8916 (pm20) cc_final: 0.8534 (pm20) REVERT: C 171 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7767 (p) REVERT: H 9 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8456 (tp30) REVERT: H 13 LYS cc_start: 0.8386 (mmmt) cc_final: 0.8089 (mmmt) REVERT: H 74 ASP cc_start: 0.8575 (t0) cc_final: 0.8183 (t0) REVERT: L 55 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8827 (mp0) REVERT: L 81 GLN cc_start: 0.8269 (mm110) cc_final: 0.8024 (mm110) outliers start: 43 outliers final: 24 residues processed: 169 average time/residue: 0.4989 time to fit residues: 88.9084 Evaluate side-chains 157 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 10.0000 chunk 57 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 0.0020 chunk 14 optimal weight: 7.9990 overall best weight: 2.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN C 247 GLN H 6 GLN L 39 GLN ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.081543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.055768 restraints weight = 14789.098| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.14 r_work: 0.2615 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7199 Z= 0.147 Angle : 0.618 9.696 9816 Z= 0.308 Chirality : 0.043 0.143 1083 Planarity : 0.004 0.046 1257 Dihedral : 5.829 52.048 974 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.81 % Favored : 93.08 % Rotamer: Outliers : 5.22 % Allowed : 25.16 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.27), residues: 881 helix: -1.80 (0.67), residues: 54 sheet: 0.04 (0.30), residues: 293 loop : -1.17 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 118 TYR 0.010 0.001 TYR L 51 PHE 0.012 0.001 PHE H 80 TRP 0.008 0.001 TRP H 48 HIS 0.003 0.000 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 7197) covalent geometry : angle 0.61815 / 0.31 ( 9812) SS BOND : bond 0.00362 / 0.17 ( 2) SS BOND : angle 0.35871 / 0.21 ( 4) hydrogen bonds : bond 0.03098 / 1.99 ( 201) hydrogen bonds : angle 5.24468 / 3.58 ( 549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: A 227 GLU cc_start: 0.7522 (pp20) cc_final: 0.7084 (pp20) REVERT: A 229 GLN cc_start: 0.8558 (mm-40) cc_final: 0.7980 (mm110) REVERT: A 238 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8181 (mtt90) REVERT: B 116 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.8892 (mptm) REVERT: B 225 MET cc_start: 0.6876 (mpt) cc_final: 0.6610 (mpp) REVERT: C 50 GLU cc_start: 0.8944 (pm20) cc_final: 0.8571 (pm20) REVERT: C 171 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7851 (p) REVERT: H 9 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8493 (tp30) REVERT: H 13 LYS cc_start: 0.8314 (mmmt) cc_final: 0.8079 (mmmt) REVERT: H 44 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8826 (mtmm) REVERT: H 74 ASP cc_start: 0.8567 (t0) cc_final: 0.8171 (t0) REVERT: L 55 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8803 (mp0) REVERT: L 81 GLN cc_start: 0.8316 (mm110) cc_final: 0.8092 (mm110) outliers start: 40 outliers final: 18 residues processed: 170 average time/residue: 0.4606 time to fit residues: 82.6049 Evaluate side-chains 156 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 69 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN C 247 GLN H 6 GLN ** L 41 HIS ** 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 = 0.3203 r_free = 0.3203 target = 0.079721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.053848 restraints weight = 14728.521| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.11 r_work: 0.2571 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7199 Z= 0.220 Angle : 0.653 9.926 9816 Z= 0.326 Chirality : 0.045 0.157 1083 Planarity : 0.005 0.051 1257 Dihedral : 5.695 48.051 974 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.38 % Favored : 92.51 % Rotamer: Outliers : 5.08 % Allowed : 25.81 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.28), residues: 881 helix: -1.94 (0.62), residues: 60 sheet: 0.04 (0.30), residues: 292 loop : -1.07 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 118 TYR 0.011 0.001 TYR L 89 PHE 0.014 0.001 PHE H 80 TRP 0.007 0.001 TRP H 48 HIS 0.012 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 ( 7197) covalent geometry : angle 0.65345 / 0.33 ( 9812) SS BOND : bond 0.00473 / 0.23 ( 2) SS BOND : angle 0.31063 / 0.18 ( 4) hydrogen bonds : bond 0.03290 / 2.14 ( 201) hydrogen bonds : angle 5.27331 / 3.60 ( 549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8200 (tp30) REVERT: A 158 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 227 GLU cc_start: 0.7539 (pp20) cc_final: 0.7074 (pp20) REVERT: A 229 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8031 (mm110) REVERT: B 116 LYS cc_start: 0.9518 (OUTLIER) cc_final: 0.8889 (mptm) REVERT: C 50 GLU cc_start: 0.8974 (pm20) cc_final: 0.8594 (pm20) REVERT: C 171 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7921 (p) REVERT: C 175 TYR cc_start: 0.8567 (m-80) cc_final: 0.8352 (m-80) REVERT: H 1 GLN cc_start: 0.8342 (tp-100) cc_final: 0.8079 (tp-100) REVERT: H 9 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8523 (tp30) REVERT: H 74 ASP cc_start: 0.8628 (t0) cc_final: 0.8198 (t0) REVERT: H 112 VAL cc_start: 0.9438 (p) cc_final: 0.9222 (m) REVERT: L 55 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8758 (mp0) REVERT: L 81 GLN cc_start: 0.8280 (mm110) cc_final: 0.8053 (mm110) outliers start: 39 outliers final: 24 residues processed: 166 average time/residue: 0.5259 time to fit residues: 91.8318 Evaluate side-chains 162 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN C 247 GLN H 6 GLN ** L 41 HIS ** 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 = 0.3217 r_free = 0.3217 target = 0.080368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.054781 restraints weight = 14823.020| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.10 r_work: 0.2577 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7199 Z= 0.140 Angle : 0.641 10.130 9816 Z= 0.318 Chirality : 0.043 0.146 1083 Planarity : 0.005 0.045 1257 Dihedral : 5.503 45.664 973 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 5.22 % Allowed : 26.34 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.28), residues: 881 helix: -1.20 (0.73), residues: 48 sheet: 0.05 (0.30), residues: 294 loop : -1.00 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 118 TYR 0.014 0.001 TYR L 89 PHE 0.011 0.001 PHE H 80 TRP 0.008 0.001 TRP H 48 HIS 0.010 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7197) covalent geometry : angle 0.64096 / 0.32 ( 9812) SS BOND : bond 0.00343 / 0.17 ( 2) SS BOND : angle 0.41407 / 0.24 ( 4) hydrogen bonds : bond 0.03006 / 1.95 ( 201) hydrogen bonds : angle 5.16477 / 3.52 ( 549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8169 (tp30) REVERT: A 158 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 227 GLU cc_start: 0.7520 (pp20) cc_final: 0.7045 (pp20) REVERT: A 229 GLN cc_start: 0.8575 (mm-40) cc_final: 0.7971 (mm110) REVERT: A 238 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8183 (mtt90) REVERT: B 116 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.8896 (mptm) REVERT: C 50 GLU cc_start: 0.8959 (pm20) cc_final: 0.8594 (pm20) REVERT: H 1 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8207 (tp-100) REVERT: H 9 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8520 (tp30) REVERT: H 74 ASP cc_start: 0.8596 (t0) cc_final: 0.8183 (t0) REVERT: H 112 VAL cc_start: 0.9409 (p) cc_final: 0.9196 (m) REVERT: L 55 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8770 (mp0) REVERT: L 81 GLN cc_start: 0.8344 (mm110) cc_final: 0.8104 (mm110) outliers start: 40 outliers final: 26 residues processed: 171 average time/residue: 0.5353 time to fit residues: 96.1838 Evaluate side-chains 165 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN C 247 GLN ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.054719 restraints weight = 14709.491| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.08 r_work: 0.2594 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7199 Z= 0.152 Angle : 0.651 10.412 9816 Z= 0.321 Chirality : 0.044 0.143 1083 Planarity : 0.005 0.047 1257 Dihedral : 5.454 44.444 973 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.69 % Allowed : 26.99 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.28), residues: 881 helix: -1.21 (0.73), residues: 48 sheet: 0.05 (0.29), residues: 298 loop : -0.97 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 118 TYR 0.015 0.001 TYR L 89 PHE 0.011 0.001 PHE H 80 TRP 0.008 0.001 TRP H 48 HIS 0.009 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7197) covalent geometry : angle 0.65116 / 0.32 ( 9812) SS BOND : bond 0.00325 / 0.16 ( 2) SS BOND : angle 0.33100 / 0.19 ( 4) hydrogen bonds : bond 0.03000 / 1.94 ( 201) hydrogen bonds : angle 5.10971 / 3.49 ( 549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8186 (tp30) REVERT: A 158 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 227 GLU cc_start: 0.7511 (pp20) cc_final: 0.7012 (pp20) REVERT: A 229 GLN cc_start: 0.8573 (mm-40) cc_final: 0.7949 (mm110) REVERT: A 238 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8202 (mtt90) REVERT: B 116 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.8901 (mptm) REVERT: B 225 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.5996 (pmm) REVERT: C 50 GLU cc_start: 0.8957 (pm20) cc_final: 0.8566 (pm20) REVERT: C 171 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8331 (t) REVERT: H 9 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8506 (tp30) REVERT: H 74 ASP cc_start: 0.8603 (t0) cc_final: 0.8185 (t0) REVERT: L 55 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8771 (mp0) REVERT: L 81 GLN cc_start: 0.8307 (mm110) cc_final: 0.8079 (mm110) outliers start: 36 outliers final: 23 residues processed: 165 average time/residue: 0.5479 time to fit residues: 95.1266 Evaluate side-chains 165 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 87 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.0070 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN C 247 GLN ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.079828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.054274 restraints weight = 14879.565| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.09 r_work: 0.2576 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7199 Z= 0.178 Angle : 0.676 10.900 9816 Z= 0.333 Chirality : 0.044 0.147 1083 Planarity : 0.005 0.050 1257 Dihedral : 5.466 43.630 973 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.56 % Allowed : 27.64 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.28), residues: 881 helix: -1.16 (0.73), residues: 48 sheet: 0.05 (0.29), residues: 298 loop : -0.94 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 118 TYR 0.017 0.001 TYR L 89 PHE 0.012 0.001 PHE H 80 TRP 0.009 0.001 TRP H 48 HIS 0.009 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 7197) covalent geometry : angle 0.67594 / 0.33 ( 9812) SS BOND : bond 0.00397 / 0.19 ( 2) SS BOND : angle 0.37771 / 0.22 ( 4) hydrogen bonds : bond 0.03048 / 1.99 ( 201) hydrogen bonds : angle 5.10214 / 3.49 ( 549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: A 158 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 227 GLU cc_start: 0.7543 (pp20) cc_final: 0.7065 (pp20) REVERT: A 229 GLN cc_start: 0.8567 (mm-40) cc_final: 0.7951 (mm110) REVERT: B 116 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.8905 (mptm) REVERT: C 50 GLU cc_start: 0.8966 (pm20) cc_final: 0.8565 (pm20) REVERT: C 83 ASN cc_start: 0.8310 (t0) cc_final: 0.8082 (t0) REVERT: C 171 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8436 (t) REVERT: H 13 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7690 (mmmt) REVERT: H 74 ASP cc_start: 0.8626 (t0) cc_final: 0.8205 (t0) REVERT: L 55 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8787 (mp0) REVERT: L 81 GLN cc_start: 0.8325 (mm110) cc_final: 0.8082 (mm110) outliers start: 35 outliers final: 23 residues processed: 163 average time/residue: 0.5431 time to fit residues: 92.9674 Evaluate side-chains 162 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN C 247 GLN ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.054484 restraints weight = 14815.194| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.08 r_work: 0.2582 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7199 Z= 0.163 Angle : 0.703 11.651 9816 Z= 0.345 Chirality : 0.044 0.172 1083 Planarity : 0.005 0.056 1257 Dihedral : 5.484 42.854 973 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.17 % Allowed : 28.42 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.28), residues: 881 helix: -1.11 (0.74), residues: 48 sheet: 0.08 (0.29), residues: 298 loop : -0.93 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 118 TYR 0.015 0.001 TYR L 89 PHE 0.011 0.001 PHE H 80 TRP 0.008 0.001 TRP H 48 HIS 0.009 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 7197) covalent geometry : angle 0.70348 / 0.34 ( 9812) SS BOND : bond 0.00350 / 0.17 ( 2) SS BOND : angle 0.35381 / 0.20 ( 4) hydrogen bonds : bond 0.02983 / 1.95 ( 201) hydrogen bonds : angle 5.05754 / 3.46 ( 549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: A 158 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 227 GLU cc_start: 0.7511 (pp20) cc_final: 0.7056 (pp20) REVERT: A 229 GLN cc_start: 0.8551 (mm-40) cc_final: 0.7948 (mm110) REVERT: B 92 PHE cc_start: 0.8487 (t80) cc_final: 0.8248 (t80) REVERT: B 116 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.8904 (mptm) REVERT: B 225 MET cc_start: 0.6996 (tpp) cc_final: 0.5852 (pmm) REVERT: C 50 GLU cc_start: 0.8964 (pm20) cc_final: 0.8575 (pm20) REVERT: C 83 ASN cc_start: 0.8277 (t0) cc_final: 0.8055 (t0) REVERT: C 171 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8433 (t) REVERT: H 1 GLN cc_start: 0.8341 (tp40) cc_final: 0.8130 (tp-100) REVERT: H 13 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7676 (mmmt) REVERT: H 74 ASP cc_start: 0.8625 (t0) cc_final: 0.8222 (t0) REVERT: H 112 VAL cc_start: 0.9449 (p) cc_final: 0.9186 (m) REVERT: L 55 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8782 (mp0) REVERT: L 81 GLN cc_start: 0.8328 (mm110) cc_final: 0.8065 (mm110) outliers start: 32 outliers final: 24 residues processed: 160 average time/residue: 0.5309 time to fit residues: 89.4492 Evaluate side-chains 162 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN ** L 41 HIS ** 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 = 0.3187 r_free = 0.3187 target = 0.078728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.053259 restraints weight = 14794.611| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.08 r_work: 0.2546 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7199 Z= 0.224 Angle : 0.726 12.035 9816 Z= 0.356 Chirality : 0.045 0.155 1083 Planarity : 0.005 0.057 1257 Dihedral : 5.570 42.475 973 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.52 % Allowed : 29.20 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.28), residues: 881 helix: -1.08 (0.74), residues: 48 sheet: 0.10 (0.30), residues: 294 loop : -0.93 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 118 TYR 0.014 0.001 TYR L 89 PHE 0.014 0.001 PHE H 80 TRP 0.007 0.001 TRP H 113 HIS 0.009 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 ( 7197) covalent geometry : angle 0.72595 / 0.36 ( 9812) SS BOND : bond 0.00477 / 0.23 ( 2) SS BOND : angle 0.42468 / 0.24 ( 4) hydrogen bonds : bond 0.03167 / 2.08 ( 201) hydrogen bonds : angle 5.06980 / 3.49 ( 549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: A 158 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 227 GLU cc_start: 0.7535 (pp20) cc_final: 0.7046 (pp20) REVERT: A 229 GLN cc_start: 0.8592 (mm-40) cc_final: 0.7956 (mm110) REVERT: B 92 PHE cc_start: 0.8508 (t80) cc_final: 0.8291 (t80) REVERT: B 116 LYS cc_start: 0.9527 (OUTLIER) cc_final: 0.8915 (mptm) REVERT: B 225 MET cc_start: 0.7047 (tpp) cc_final: 0.5926 (pmm) REVERT: C 50 GLU cc_start: 0.8972 (pm20) cc_final: 0.8570 (pm20) REVERT: C 83 ASN cc_start: 0.8328 (t0) cc_final: 0.8121 (t0) REVERT: C 171 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8507 (t) REVERT: H 74 ASP cc_start: 0.8676 (t0) cc_final: 0.8270 (t0) REVERT: L 55 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8865 (mp0) REVERT: L 81 GLN cc_start: 0.8346 (mm110) cc_final: 0.8088 (mm110) outliers start: 27 outliers final: 25 residues processed: 152 average time/residue: 0.5792 time to fit residues: 92.6900 Evaluate side-chains 158 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN C 152 HIS ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.054457 restraints weight = 14711.743| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.06 r_work: 0.2594 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7199 Z= 0.159 Angle : 0.705 12.116 9816 Z= 0.346 Chirality : 0.044 0.159 1083 Planarity : 0.005 0.060 1257 Dihedral : 5.508 41.603 973 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.52 % Allowed : 28.94 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.28), residues: 881 helix: -1.06 (0.74), residues: 48 sheet: 0.09 (0.30), residues: 297 loop : -0.90 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 118 TYR 0.011 0.001 TYR L 51 PHE 0.011 0.001 PHE H 80 TRP 0.009 0.001 TRP H 48 HIS 0.008 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 7197) covalent geometry : angle 0.70514 / 0.35 ( 9812) SS BOND : bond 0.00361 / 0.17 ( 2) SS BOND : angle 0.42487 / 0.25 ( 4) hydrogen bonds : bond 0.02997 / 1.96 ( 201) hydrogen bonds : angle 4.96564 / 3.41 ( 549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2848.49 seconds wall clock time: 49 minutes 21.98 seconds (2961.98 seconds total)