Starting phenix.real_space_refine on Fri Aug 22 20:35:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b79_44304/08_2025/9b79_44304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b79_44304/08_2025/9b79_44304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b79_44304/08_2025/9b79_44304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b79_44304/08_2025/9b79_44304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b79_44304/08_2025/9b79_44304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b79_44304/08_2025/9b79_44304.map" } resolution = 2.71 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= 0.001 sd= 0.040 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 28 5.16 5 C 4960 2.51 5 N 1412 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7876 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "B" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "C" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "D" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Time building chain proxies: 1.69, per 1000 atoms: 0.21 Number of scatterers: 7876 At special positions: 0 Unit cell: (104.076, 82.6, 103.25, 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 28 16.00 O 1476 8.00 N 1412 7.00 C 4960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 402.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1912 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 8 sheets defined 47.3% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.686A pdb=" N GLU A 56 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 58 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 124 Processing helix chain 'A' and resid 155 through 167 removed outlier: 3.659A pdb=" N SER A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 213 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 39 through 52 Processing helix chain 'B' and resid 53 through 57 removed outlier: 3.650A pdb=" N GLU B 56 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 removed outlier: 4.029A pdb=" N TRP B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 109 through 124 Processing helix chain 'B' and resid 155 through 167 removed outlier: 3.774A pdb=" N SER B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 213 removed outlier: 3.706A pdb=" N PHE B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.715A pdb=" N LEU B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 39 through 52 Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.891A pdb=" N GLU C 56 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.644A pdb=" N VAL C 108 " --> pdb=" O PRO C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 124 Processing helix chain 'C' and resid 155 through 167 Processing helix chain 'C' and resid 185 through 213 removed outlier: 3.620A pdb=" N PHE C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 235 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 39 through 52 Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.705A pdb=" N GLU D 56 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 4.076A pdb=" N TRP D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.527A pdb=" N VAL D 108 " --> pdb=" O PRO D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 124 Processing helix chain 'D' and resid 155 through 167 removed outlier: 3.648A pdb=" N SER D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 213 Processing helix chain 'D' and resid 230 through 235 removed outlier: 3.701A pdb=" N LEU D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 33 removed outlier: 5.533A pdb=" N VAL A 26 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 18 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 28 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 61 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE A 90 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA A 63 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 154 removed outlier: 4.042A pdb=" N GLY A 149 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 126 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A 225 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 128 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 227 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 130 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 33 removed outlier: 5.382A pdb=" N VAL B 26 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER B 18 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER B 65 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 154 removed outlier: 4.087A pdb=" N GLY B 149 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N HIS B 243 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 224 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 33 removed outlier: 6.901A pdb=" N LEU C 16 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN C 29 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL C 14 " --> pdb=" O GLN C 29 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG C 31 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR C 12 " --> pdb=" O ARG C 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 154 removed outlier: 4.013A pdb=" N GLY C 149 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 33 removed outlier: 5.362A pdb=" N VAL D 26 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER D 18 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR D 61 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE D 90 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA D 63 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 147 through 154 removed outlier: 4.060A pdb=" N GLY D 149 " --> pdb=" O VAL D 140 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1326 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: 1.22 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: 1.22 - 1.34: 2716 1.34 - 1.46: 1054 1.46 - 1.57: 4190 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 8004 Sorted by residual: bond pdb=" CB ASN A 104 " pdb=" CG ASN A 104 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.60e+00 bond pdb=" CB ASN C 104 " pdb=" CG ASN C 104 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.50e+00 bond pdb=" CB ASN D 104 " pdb=" CG ASN D 104 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.49e+00 bond pdb=" CA VAL C 102 " pdb=" CB VAL C 102 " ideal model delta sigma weight residual 1.546 1.565 -0.019 1.69e-02 3.50e+03 1.24e+00 bond pdb=" CB VAL D 114 " pdb=" CG1 VAL D 114 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 ... (remaining 7999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10651 1.62 - 3.25: 197 3.25 - 4.87: 29 4.87 - 6.49: 9 6.49 - 8.11: 6 Bond angle restraints: 10892 Sorted by residual: angle pdb=" C ASN A 104 " pdb=" CA ASN A 104 " pdb=" CB ASN A 104 " ideal model delta sigma weight residual 111.20 116.50 -5.30 1.81e+00 3.05e-01 8.57e+00 angle pdb=" C ASN B 104 " pdb=" CA ASN B 104 " pdb=" CB ASN B 104 " ideal model delta sigma weight residual 111.20 116.48 -5.28 1.81e+00 3.05e-01 8.50e+00 angle pdb=" C ASN C 104 " pdb=" CA ASN C 104 " pdb=" CB ASN C 104 " ideal model delta sigma weight residual 111.29 116.39 -5.10 1.92e+00 2.71e-01 7.06e+00 angle pdb=" C ASN D 104 " pdb=" CA ASN D 104 " pdb=" CB ASN D 104 " ideal model delta sigma weight residual 111.29 116.26 -4.97 1.92e+00 2.71e-01 6.69e+00 angle pdb=" CA ASN A 104 " pdb=" CB ASN A 104 " pdb=" CG ASN A 104 " ideal model delta sigma weight residual 112.60 115.07 -2.47 1.00e+00 1.00e+00 6.11e+00 ... (remaining 10887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 4437 16.74 - 33.49: 293 33.49 - 50.23: 48 50.23 - 66.98: 18 66.98 - 83.72: 4 Dihedral angle restraints: 4800 sinusoidal: 1836 harmonic: 2964 Sorted by residual: dihedral pdb=" CA GLN B 80 " pdb=" C GLN B 80 " pdb=" N TYR B 81 " pdb=" CA TYR B 81 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASP A 131 " pdb=" CB ASP A 131 " pdb=" CG ASP A 131 " pdb=" OD1 ASP A 131 " ideal model delta sinusoidal sigma weight residual -30.00 -87.65 57.65 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA GLN D 80 " pdb=" C GLN D 80 " pdb=" N TYR D 81 " pdb=" CA TYR D 81 " ideal model delta harmonic sigma weight residual -180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 888 0.042 - 0.085: 296 0.085 - 0.127: 110 0.127 - 0.170: 20 0.170 - 0.212: 6 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA VAL C 102 " pdb=" N VAL C 102 " pdb=" C VAL C 102 " pdb=" CB VAL C 102 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ASN B 104 " pdb=" N ASN B 104 " pdb=" C ASN B 104 " pdb=" CB ASN B 104 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ASN A 104 " pdb=" N ASN A 104 " pdb=" C ASN A 104 " pdb=" CB ASN A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 1317 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 194 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA D 194 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA D 194 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL D 195 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 193 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C GLY B 193 " -0.033 2.00e-02 2.50e+03 pdb=" O GLY B 193 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA B 194 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 193 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C GLY C 193 " 0.029 2.00e-02 2.50e+03 pdb=" O GLY C 193 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA C 194 " -0.010 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1114 2.76 - 3.30: 7260 3.30 - 3.83: 13112 3.83 - 4.37: 15211 4.37 - 4.90: 27160 Nonbonded interactions: 63857 Sorted by model distance: nonbonded pdb=" NH2 ARG C 8 " pdb=" OD2 ASP C 131 " model vdw 2.229 3.120 nonbonded pdb=" ND2 ASN D 115 " pdb=" OD2 ASP D 131 " model vdw 2.261 3.120 nonbonded pdb=" NH2 ARG A 75 " pdb=" OE2 GLU A 91 " model vdw 2.280 3.120 nonbonded pdb=" O GLU C 237 " pdb=" NH2 ARG D 208 " model vdw 2.320 3.120 nonbonded pdb=" O GLY C 155 " pdb=" OG SER C 159 " model vdw 2.324 3.040 ... (remaining 63852 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 7.810 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 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 0.035 8004 Z= 0.136 Angle : 0.596 8.113 10892 Z= 0.315 Chirality : 0.050 0.212 1320 Planarity : 0.005 0.038 1412 Dihedral : 12.077 83.724 2888 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.26), residues: 1036 helix: 1.36 (0.25), residues: 408 sheet: 0.93 (0.35), residues: 228 loop : -0.25 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 171 TYR 0.008 0.001 TYR D 120 PHE 0.019 0.001 PHE B 147 TRP 0.007 0.001 TRP A 30 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8004) covalent geometry : angle 0.59612 (10892) hydrogen bonds : bond 0.11781 ( 468) hydrogen bonds : angle 6.07238 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.298 Fit side-chains REVERT: A 25 LYS cc_start: 0.7560 (pttt) cc_final: 0.7278 (tptt) REVERT: A 75 ARG cc_start: 0.6081 (mtt180) cc_final: 0.5831 (tpp-160) REVERT: A 246 GLN cc_start: 0.6610 (pt0) cc_final: 0.6126 (tt0) REVERT: B 20 MET cc_start: 0.6680 (pmm) cc_final: 0.6233 (pmm) REVERT: B 25 LYS cc_start: 0.7267 (pttt) cc_final: 0.6611 (ptmt) REVERT: B 48 ASP cc_start: 0.6119 (t0) cc_final: 0.5889 (m-30) REVERT: B 142 SER cc_start: 0.8149 (m) cc_final: 0.7755 (p) REVERT: D 1 MET cc_start: 0.4395 (mmp) cc_final: 0.3701 (ttt) REVERT: D 18 SER cc_start: 0.7385 (t) cc_final: 0.7152 (m) REVERT: D 20 MET cc_start: 0.4723 (pmm) cc_final: 0.4394 (pmm) REVERT: D 25 LYS cc_start: 0.7564 (pttt) cc_final: 0.7217 (ptmt) REVERT: D 29 GLN cc_start: 0.5952 (tt0) cc_final: 0.5569 (tm-30) REVERT: D 106 LYS cc_start: 0.7301 (mttt) cc_final: 0.6355 (mppt) REVERT: D 208 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7286 (mtt-85) REVERT: D 246 GLN cc_start: 0.7598 (pt0) cc_final: 0.7175 (tt0) REVERT: D 258 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6578 (tt0) outliers start: 0 outliers final: 1 residues processed: 175 average time/residue: 0.5428 time to fit residues: 99.9486 Evaluate side-chains 117 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 HIS B 9 ASN B 28 GLN C 247 HIS D 9 ASN D 247 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.219281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.181862 restraints weight = 8284.416| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.00 r_work: 0.4068 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3943 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8004 Z= 0.173 Angle : 0.588 6.175 10892 Z= 0.309 Chirality : 0.047 0.148 1320 Planarity : 0.005 0.034 1412 Dihedral : 4.276 20.861 1126 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.13 % Allowed : 14.15 % Favored : 81.72 % 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 aren not related in a simple way. whole: 1.25 (0.26), residues: 1036 helix: 1.60 (0.25), residues: 416 sheet: 0.96 (0.35), residues: 228 loop : 0.01 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 57 TYR 0.009 0.001 TYR D 120 PHE 0.012 0.002 PHE B 198 TRP 0.007 0.001 TRP B 82 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8004) covalent geometry : angle 0.58765 (10892) hydrogen bonds : bond 0.04136 ( 468) hydrogen bonds : angle 5.18643 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.246 Fit side-chains REVERT: A 56 GLU cc_start: 0.7306 (mp0) cc_final: 0.6876 (mp0) REVERT: A 89 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4958 (tp) REVERT: A 90 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6403 (pp) REVERT: A 246 GLN cc_start: 0.6574 (pt0) cc_final: 0.6114 (tt0) REVERT: B 20 MET cc_start: 0.6985 (pmm) cc_final: 0.6519 (pmm) REVERT: B 25 LYS cc_start: 0.7940 (pttt) cc_final: 0.7482 (pttt) REVERT: B 121 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: D 1 MET cc_start: 0.5264 (mmp) cc_final: 0.4529 (ttm) REVERT: D 29 GLN cc_start: 0.6174 (tt0) cc_final: 0.5905 (tm-30) REVERT: D 106 LYS cc_start: 0.8031 (mttt) cc_final: 0.7511 (mppt) REVERT: D 246 GLN cc_start: 0.7899 (pt0) cc_final: 0.7443 (tt0) REVERT: D 258 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7211 (tt0) outliers start: 35 outliers final: 15 residues processed: 138 average time/residue: 0.6257 time to fit residues: 90.6273 Evaluate side-chains 125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 9 ASN D 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.217472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.179350 restraints weight = 8194.842| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.05 r_work: 0.4029 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8004 Z= 0.195 Angle : 0.609 6.231 10892 Z= 0.318 Chirality : 0.048 0.162 1320 Planarity : 0.004 0.035 1412 Dihedral : 4.316 16.526 1124 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.31 % Allowed : 15.92 % Favored : 78.77 % 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 aren not related in a simple way. whole: 1.18 (0.26), residues: 1036 helix: 1.59 (0.25), residues: 416 sheet: 0.79 (0.35), residues: 228 loop : 0.01 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 57 TYR 0.010 0.002 TYR D 120 PHE 0.014 0.002 PHE B 198 TRP 0.009 0.002 TRP B 82 HIS 0.008 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 8004) covalent geometry : angle 0.60878 (10892) hydrogen bonds : bond 0.04228 ( 468) hydrogen bonds : angle 5.18957 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 0.285 Fit side-chains REVERT: A 56 GLU cc_start: 0.7345 (mp0) cc_final: 0.6959 (mp0) REVERT: A 75 ARG cc_start: 0.6706 (tpp-160) cc_final: 0.6243 (tpm170) REVERT: A 166 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6409 (ttp80) REVERT: A 246 GLN cc_start: 0.6580 (pt0) cc_final: 0.6152 (tt0) REVERT: A 260 ASN cc_start: 0.5522 (OUTLIER) cc_final: 0.5216 (m-40) REVERT: B 20 MET cc_start: 0.6961 (pmm) cc_final: 0.6509 (pmm) REVERT: B 25 LYS cc_start: 0.8055 (pttt) cc_final: 0.7559 (pttt) REVERT: B 175 LEU cc_start: 0.7096 (tp) cc_final: 0.6846 (mm) REVERT: B 237 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7223 (mm-30) REVERT: C 57 ARG cc_start: 0.6989 (ttp-110) cc_final: 0.6398 (mtm180) REVERT: D 1 MET cc_start: 0.5480 (mmp) cc_final: 0.4664 (ttm) REVERT: D 29 GLN cc_start: 0.6297 (tt0) cc_final: 0.5968 (tm-30) REVERT: D 33 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7483 (mpt180) REVERT: D 106 LYS cc_start: 0.8146 (mttt) cc_final: 0.7674 (mppt) REVERT: D 246 GLN cc_start: 0.7926 (pt0) cc_final: 0.7477 (tt0) REVERT: D 258 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7233 (tt0) outliers start: 45 outliers final: 23 residues processed: 135 average time/residue: 0.5694 time to fit residues: 81.0364 Evaluate side-chains 129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.221178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.183606 restraints weight = 8321.283| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.00 r_work: 0.4088 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8004 Z= 0.118 Angle : 0.537 6.742 10892 Z= 0.276 Chirality : 0.045 0.140 1320 Planarity : 0.004 0.033 1412 Dihedral : 3.938 17.131 1124 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.89 % Allowed : 18.63 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.27), residues: 1036 helix: 2.02 (0.26), residues: 416 sheet: 0.38 (0.34), residues: 248 loop : 0.25 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 57 TYR 0.008 0.001 TYR D 120 PHE 0.010 0.001 PHE A 198 TRP 0.009 0.001 TRP B 30 HIS 0.003 0.000 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8004) covalent geometry : angle 0.53721 (10892) hydrogen bonds : bond 0.03416 ( 468) hydrogen bonds : angle 4.86774 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7437 (mp0) cc_final: 0.7088 (mp0) REVERT: A 124 ARG cc_start: 0.6163 (mmt180) cc_final: 0.5909 (mpt-90) REVERT: A 246 GLN cc_start: 0.6498 (pt0) cc_final: 0.6000 (tt0) REVERT: B 20 MET cc_start: 0.6893 (pmm) cc_final: 0.6453 (pmm) REVERT: B 25 LYS cc_start: 0.8032 (pttt) cc_final: 0.7538 (pttt) REVERT: B 121 ASP cc_start: 0.7681 (t70) cc_final: 0.7403 (t70) REVERT: B 175 LEU cc_start: 0.7087 (tp) cc_final: 0.6806 (mm) REVERT: B 237 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: D 1 MET cc_start: 0.5373 (mmp) cc_final: 0.4686 (ttm) REVERT: D 29 GLN cc_start: 0.6225 (tt0) cc_final: 0.5973 (tm-30) REVERT: D 106 LYS cc_start: 0.8153 (mttt) cc_final: 0.7682 (mppt) REVERT: D 246 GLN cc_start: 0.7825 (pt0) cc_final: 0.7419 (tt0) REVERT: D 259 ARG cc_start: 0.6618 (ttm110) cc_final: 0.5891 (ptp90) outliers start: 33 outliers final: 19 residues processed: 137 average time/residue: 0.5754 time to fit residues: 82.7409 Evaluate side-chains 129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 214 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 92 optimal weight: 0.0470 chunk 63 optimal weight: 5.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 29 GLN B 260 ASN D 251 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.217904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.179081 restraints weight = 8352.862| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.04 r_work: 0.4040 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8004 Z= 0.179 Angle : 0.615 10.887 10892 Z= 0.315 Chirality : 0.047 0.143 1320 Planarity : 0.004 0.046 1412 Dihedral : 4.176 16.534 1124 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.42 % Allowed : 19.81 % Favored : 74.76 % 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 aren not related in a simple way. whole: 1.31 (0.26), residues: 1036 helix: 1.83 (0.25), residues: 416 sheet: 0.66 (0.34), residues: 232 loop : 0.06 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 57 TYR 0.010 0.001 TYR D 120 PHE 0.015 0.002 PHE B 198 TRP 0.008 0.001 TRP B 30 HIS 0.005 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8004) covalent geometry : angle 0.61533 (10892) hydrogen bonds : bond 0.03999 ( 468) hydrogen bonds : angle 5.07445 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7536 (mp0) cc_final: 0.7160 (mp0) REVERT: A 246 GLN cc_start: 0.6556 (pt0) cc_final: 0.6122 (tt0) REVERT: A 260 ASN cc_start: 0.5516 (OUTLIER) cc_final: 0.5162 (m-40) REVERT: B 20 MET cc_start: 0.6904 (pmm) cc_final: 0.6180 (pmm) REVERT: B 23 HIS cc_start: 0.6713 (m90) cc_final: 0.6499 (m90) REVERT: B 25 LYS cc_start: 0.8024 (pttt) cc_final: 0.7516 (pttt) REVERT: B 29 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: B 121 ASP cc_start: 0.7697 (t70) cc_final: 0.7406 (t70) REVERT: B 175 LEU cc_start: 0.7176 (tp) cc_final: 0.6911 (mm) REVERT: B 237 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: C 57 ARG cc_start: 0.7007 (ttp-110) cc_final: 0.6469 (mtm180) REVERT: D 1 MET cc_start: 0.5398 (mmp) cc_final: 0.4639 (ttm) REVERT: D 29 GLN cc_start: 0.6331 (tt0) cc_final: 0.5993 (tm-30) REVERT: D 33 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.7513 (mpt180) REVERT: D 106 LYS cc_start: 0.8209 (mttt) cc_final: 0.7735 (mppt) REVERT: D 246 GLN cc_start: 0.7828 (pt0) cc_final: 0.7389 (tt0) REVERT: D 259 ARG cc_start: 0.6676 (ttm110) cc_final: 0.5932 (ptp90) outliers start: 46 outliers final: 28 residues processed: 140 average time/residue: 0.6460 time to fit residues: 95.0956 Evaluate side-chains 141 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 0.3980 chunk 92 optimal weight: 0.0870 chunk 2 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN D 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.219715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.181676 restraints weight = 8250.134| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.00 r_work: 0.4074 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8004 Z= 0.136 Angle : 0.583 11.294 10892 Z= 0.296 Chirality : 0.045 0.140 1320 Planarity : 0.004 0.044 1412 Dihedral : 4.024 16.795 1124 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.25 % Allowed : 20.87 % Favored : 74.88 % 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 aren not related in a simple way. whole: 1.45 (0.26), residues: 1036 helix: 1.98 (0.26), residues: 416 sheet: 0.67 (0.34), residues: 232 loop : 0.12 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 57 TYR 0.008 0.001 TYR D 120 PHE 0.010 0.001 PHE C 132 TRP 0.008 0.001 TRP B 30 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8004) covalent geometry : angle 0.58286 (10892) hydrogen bonds : bond 0.03586 ( 468) hydrogen bonds : angle 4.93832 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7527 (mp0) cc_final: 0.7144 (mp0) REVERT: A 246 GLN cc_start: 0.6540 (pt0) cc_final: 0.6064 (tt0) REVERT: A 260 ASN cc_start: 0.5572 (OUTLIER) cc_final: 0.5147 (m-40) REVERT: B 20 MET cc_start: 0.6871 (pmm) cc_final: 0.6451 (pmm) REVERT: B 25 LYS cc_start: 0.8008 (pttt) cc_final: 0.7523 (pttt) REVERT: B 121 ASP cc_start: 0.7703 (t70) cc_final: 0.7425 (t70) REVERT: B 175 LEU cc_start: 0.7157 (tp) cc_final: 0.6867 (mm) REVERT: B 237 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: C 57 ARG cc_start: 0.7006 (ttp-110) cc_final: 0.6453 (mtm180) REVERT: D 1 MET cc_start: 0.5425 (mmp) cc_final: 0.4715 (ttm) REVERT: D 29 GLN cc_start: 0.6264 (tt0) cc_final: 0.5963 (tm-30) REVERT: D 33 ARG cc_start: 0.7830 (mtt-85) cc_final: 0.7459 (mpt180) REVERT: D 91 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5775 (mt-10) REVERT: D 106 LYS cc_start: 0.8218 (mttt) cc_final: 0.7764 (mppt) REVERT: D 246 GLN cc_start: 0.7815 (pt0) cc_final: 0.7423 (tt0) REVERT: D 259 ARG cc_start: 0.6622 (ttm110) cc_final: 0.5895 (ptp90) outliers start: 36 outliers final: 23 residues processed: 131 average time/residue: 0.6322 time to fit residues: 86.8718 Evaluate side-chains 133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 38 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 GLN D 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.212401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.173868 restraints weight = 8329.101| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.22 r_work: 0.3954 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 8004 Z= 0.276 Angle : 0.720 11.493 10892 Z= 0.374 Chirality : 0.052 0.186 1320 Planarity : 0.005 0.042 1412 Dihedral : 4.656 16.763 1124 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.31 % Allowed : 20.75 % Favored : 73.94 % 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 aren not related in a simple way. whole: 0.77 (0.26), residues: 1036 helix: 1.29 (0.25), residues: 416 sheet: 0.38 (0.34), residues: 232 loop : -0.12 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 57 TYR 0.013 0.002 TYR D 120 PHE 0.021 0.002 PHE B 198 TRP 0.012 0.002 TRP B 82 HIS 0.008 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 8004) covalent geometry : angle 0.72047 (10892) hydrogen bonds : bond 0.04851 ( 468) hydrogen bonds : angle 5.48772 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.314 Fit side-chains REVERT: A 56 GLU cc_start: 0.7504 (mp0) cc_final: 0.7197 (mp0) REVERT: A 166 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6083 (ttp80) REVERT: A 246 GLN cc_start: 0.6484 (pt0) cc_final: 0.6032 (tt0) REVERT: A 260 ASN cc_start: 0.5462 (OUTLIER) cc_final: 0.5103 (m-40) REVERT: B 20 MET cc_start: 0.6854 (pmm) cc_final: 0.6112 (pmm) REVERT: B 23 HIS cc_start: 0.6865 (m90) cc_final: 0.6638 (m90) REVERT: B 25 LYS cc_start: 0.8001 (pttt) cc_final: 0.7549 (ptmt) REVERT: B 29 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.7018 (tt0) REVERT: B 121 ASP cc_start: 0.7754 (t70) cc_final: 0.7496 (t70) REVERT: B 175 LEU cc_start: 0.7269 (tp) cc_final: 0.6990 (mm) REVERT: B 237 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: D 1 MET cc_start: 0.5530 (mmp) cc_final: 0.4676 (ttm) REVERT: D 29 GLN cc_start: 0.6409 (tt0) cc_final: 0.5988 (tm-30) REVERT: D 33 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7577 (mpt180) REVERT: D 106 LYS cc_start: 0.8350 (mttt) cc_final: 0.7805 (mppt) REVERT: D 246 GLN cc_start: 0.7875 (pt0) cc_final: 0.7429 (tt0) REVERT: D 259 ARG cc_start: 0.6673 (ttm110) cc_final: 0.5964 (ptp90) outliers start: 45 outliers final: 33 residues processed: 136 average time/residue: 0.5582 time to fit residues: 80.1228 Evaluate side-chains 143 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 225 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 260 ASN D 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.218289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.179499 restraints weight = 8314.880| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.09 r_work: 0.4023 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8004 Z= 0.133 Angle : 0.606 11.583 10892 Z= 0.308 Chirality : 0.045 0.142 1320 Planarity : 0.004 0.044 1412 Dihedral : 4.085 16.954 1124 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.36 % Allowed : 22.17 % Favored : 73.47 % 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 aren not related in a simple way. whole: 1.30 (0.26), residues: 1036 helix: 1.90 (0.26), residues: 412 sheet: 0.57 (0.35), residues: 232 loop : 0.02 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 57 TYR 0.011 0.001 TYR A 81 PHE 0.009 0.001 PHE B 198 TRP 0.008 0.001 TRP A 82 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8004) covalent geometry : angle 0.60587 (10892) hydrogen bonds : bond 0.03520 ( 468) hydrogen bonds : angle 5.02307 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7507 (mp0) cc_final: 0.7135 (mp0) REVERT: A 246 GLN cc_start: 0.6453 (pt0) cc_final: 0.5945 (tt0) REVERT: A 260 ASN cc_start: 0.5473 (OUTLIER) cc_final: 0.5095 (m-40) REVERT: B 20 MET cc_start: 0.6867 (pmm) cc_final: 0.6145 (pmm) REVERT: B 23 HIS cc_start: 0.6777 (m90) cc_final: 0.6521 (m90) REVERT: B 25 LYS cc_start: 0.7993 (pttt) cc_final: 0.7483 (pttt) REVERT: B 121 ASP cc_start: 0.7708 (t70) cc_final: 0.7431 (t70) REVERT: B 175 LEU cc_start: 0.7180 (tp) cc_final: 0.6868 (mm) REVERT: B 237 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: C 57 ARG cc_start: 0.7004 (ttp-110) cc_final: 0.6409 (mtm180) REVERT: D 1 MET cc_start: 0.5456 (mmp) cc_final: 0.4719 (ttm) REVERT: D 29 GLN cc_start: 0.6296 (tt0) cc_final: 0.5951 (tm-30) REVERT: D 33 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.7462 (mpt180) REVERT: D 106 LYS cc_start: 0.8302 (mttt) cc_final: 0.7767 (mppt) REVERT: D 246 GLN cc_start: 0.7730 (pt0) cc_final: 0.7326 (tt0) REVERT: D 259 ARG cc_start: 0.6555 (ttm110) cc_final: 0.5852 (ptp90) outliers start: 37 outliers final: 26 residues processed: 134 average time/residue: 0.6014 time to fit residues: 84.9553 Evaluate side-chains 136 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 36 optimal weight: 0.0170 chunk 64 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 88 optimal weight: 0.0670 chunk 85 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.221211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.183495 restraints weight = 8281.329| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.01 r_work: 0.4064 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8004 Z= 0.115 Angle : 0.595 13.522 10892 Z= 0.297 Chirality : 0.045 0.136 1320 Planarity : 0.004 0.050 1412 Dihedral : 3.787 16.941 1124 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.54 % Allowed : 23.11 % Favored : 73.35 % 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 aren not related in a simple way. whole: 1.47 (0.27), residues: 1036 helix: 2.14 (0.26), residues: 408 sheet: 0.27 (0.34), residues: 248 loop : 0.31 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 57 TYR 0.017 0.001 TYR A 81 PHE 0.010 0.001 PHE B 198 TRP 0.011 0.001 TRP B 30 HIS 0.003 0.000 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8004) covalent geometry : angle 0.59476 (10892) hydrogen bonds : bond 0.03223 ( 468) hydrogen bonds : angle 4.82993 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7523 (mp0) cc_final: 0.7146 (mp0) REVERT: A 121 ASP cc_start: 0.6815 (m-30) cc_final: 0.6313 (t0) REVERT: A 246 GLN cc_start: 0.6482 (pt0) cc_final: 0.5925 (tt0) REVERT: A 260 ASN cc_start: 0.5302 (OUTLIER) cc_final: 0.4942 (m-40) REVERT: B 20 MET cc_start: 0.6898 (pmm) cc_final: 0.6207 (pmm) REVERT: B 23 HIS cc_start: 0.6661 (m90) cc_final: 0.6443 (m90) REVERT: B 25 LYS cc_start: 0.7963 (pttt) cc_final: 0.7457 (pttt) REVERT: B 102 VAL cc_start: 0.6804 (OUTLIER) cc_final: 0.6364 (m) REVERT: B 121 ASP cc_start: 0.7656 (t70) cc_final: 0.7388 (t70) REVERT: B 175 LEU cc_start: 0.7185 (tp) cc_final: 0.6840 (mm) REVERT: B 237 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: C 22 GLU cc_start: 0.7495 (tp30) cc_final: 0.7294 (tp30) REVERT: C 57 ARG cc_start: 0.6994 (ttp-110) cc_final: 0.6474 (mtm180) REVERT: C 224 ILE cc_start: 0.8051 (mt) cc_final: 0.7546 (mm) REVERT: D 1 MET cc_start: 0.5355 (mmp) cc_final: 0.4687 (ttm) REVERT: D 29 GLN cc_start: 0.6140 (tt0) cc_final: 0.5827 (tm-30) REVERT: D 106 LYS cc_start: 0.8218 (mttt) cc_final: 0.7676 (mppt) REVERT: D 246 GLN cc_start: 0.7789 (pt0) cc_final: 0.7370 (tt0) outliers start: 30 outliers final: 19 residues processed: 138 average time/residue: 0.6060 time to fit residues: 88.0580 Evaluate side-chains 135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 251 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.218077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.177676 restraints weight = 8107.514| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.20 r_work: 0.3958 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8004 Z= 0.204 Angle : 0.680 14.908 10892 Z= 0.343 Chirality : 0.048 0.148 1320 Planarity : 0.004 0.045 1412 Dihedral : 4.142 16.312 1124 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.18 % Allowed : 23.94 % Favored : 72.88 % 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 aren not related in a simple way. whole: 1.16 (0.27), residues: 1036 helix: 1.79 (0.26), residues: 408 sheet: 0.16 (0.33), residues: 248 loop : 0.21 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 57 TYR 0.012 0.002 TYR A 81 PHE 0.016 0.002 PHE B 198 TRP 0.008 0.002 TRP B 82 HIS 0.006 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 8004) covalent geometry : angle 0.67955 (10892) hydrogen bonds : bond 0.04013 ( 468) hydrogen bonds : angle 5.12021 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7487 (mp0) cc_final: 0.7190 (mp0) REVERT: A 246 GLN cc_start: 0.6395 (pt0) cc_final: 0.5892 (tt0) REVERT: A 260 ASN cc_start: 0.5266 (OUTLIER) cc_final: 0.4931 (m-40) REVERT: B 20 MET cc_start: 0.7017 (pmm) cc_final: 0.6418 (pmm) REVERT: B 25 LYS cc_start: 0.7907 (pttt) cc_final: 0.7509 (ptmt) REVERT: B 102 VAL cc_start: 0.7062 (OUTLIER) cc_final: 0.6752 (m) REVERT: B 121 ASP cc_start: 0.7576 (t70) cc_final: 0.7364 (t70) REVERT: B 175 LEU cc_start: 0.7246 (tp) cc_final: 0.6926 (mm) REVERT: B 237 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: C 25 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8133 (mptp) REVERT: C 57 ARG cc_start: 0.7052 (ttp-110) cc_final: 0.6402 (mtm180) REVERT: C 224 ILE cc_start: 0.7985 (mt) cc_final: 0.7457 (mm) REVERT: D 1 MET cc_start: 0.5312 (mmp) cc_final: 0.4643 (ttm) REVERT: D 29 GLN cc_start: 0.6205 (tt0) cc_final: 0.5860 (tm-30) REVERT: D 33 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7617 (mpt180) REVERT: D 106 LYS cc_start: 0.8221 (mttt) cc_final: 0.7697 (mppt) REVERT: D 246 GLN cc_start: 0.7773 (pt0) cc_final: 0.7391 (tt0) outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 0.5799 time to fit residues: 75.1205 Evaluate side-chains 123 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 0.0470 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 73 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 0.0870 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.220999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.183644 restraints weight = 8218.293| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.98 r_work: 0.4070 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8004 Z= 0.118 Angle : 0.619 14.829 10892 Z= 0.306 Chirality : 0.045 0.137 1320 Planarity : 0.004 0.045 1412 Dihedral : 3.798 16.556 1124 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.95 % Allowed : 24.65 % Favored : 72.41 % 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 aren not related in a simple way. whole: 1.47 (0.27), residues: 1036 helix: 2.12 (0.27), residues: 408 sheet: 0.27 (0.34), residues: 248 loop : 0.32 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 57 TYR 0.021 0.002 TYR A 81 PHE 0.009 0.001 PHE A 198 TRP 0.012 0.001 TRP B 30 HIS 0.003 0.000 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8004) covalent geometry : angle 0.61888 (10892) hydrogen bonds : bond 0.03207 ( 468) hydrogen bonds : angle 4.83562 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.30 seconds wall clock time: 52 minutes 31.83 seconds (3151.83 seconds total)