Starting phenix.real_space_refine on Wed Mar 12 10:48:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b79_44304/03_2025/9b79_44304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b79_44304/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b79_44304/03_2025/9b79_44304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b79_44304/03_2025/9b79_44304.map" model { file = "/net/cci-nas-00/data/ceres_data/9b79_44304/03_2025/9b79_44304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b79_44304/03_2025/9b79_44304.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.44, per 1000 atoms: 0.69 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: 1.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.93 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: 2.24 Time building geometry restraints manager: 2.35 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: 0.02 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.140 Process input model: 23.300 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- 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= 0.206 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), 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 TRP 0.007 0.001 TRP A 30 HIS 0.003 0.001 HIS A 72 PHE 0.019 0.001 PHE B 147 TYR 0.008 0.001 TYR D 120 ARG 0.007 0.001 ARG C 171 *********************** 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 : 0.847 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: 1.3355 time to fit residues: 246.0844 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 : 0.993 ------------------------------------------------------------------------------- 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 87 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.0040 chunk 49 optimal weight: 0.4980 chunk 60 optimal weight: 0.0040 chunk 94 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4561 r_free = 0.4561 target = 0.221272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.183787 restraints weight = 8208.749| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.01 r_work: 0.4096 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1626 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= 0.216 Angle : 0.557 6.066 10892 Z= 0.291 Chirality : 0.046 0.143 1320 Planarity : 0.004 0.033 1412 Dihedral : 4.105 21.426 1126 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.54 % Allowed : 14.50 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1036 helix: 1.76 (0.25), residues: 416 sheet: 1.06 (0.35), residues: 228 loop : 0.06 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 30 HIS 0.003 0.001 HIS D 72 PHE 0.009 0.001 PHE C 132 TYR 0.008 0.001 TYR D 120 ARG 0.007 0.001 ARG C 57 *********************** 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 150 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.769 Fit side-chains REVERT: A 56 GLU cc_start: 0.7317 (mp0) cc_final: 0.6891 (mp0) REVERT: A 89 LEU cc_start: 0.5136 (OUTLIER) cc_final: 0.4908 (tp) REVERT: A 90 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6436 (pp) REVERT: A 124 ARG cc_start: 0.6066 (mmt180) cc_final: 0.5781 (mpt-90) REVERT: A 246 GLN cc_start: 0.6553 (pt0) cc_final: 0.6080 (tt0) REVERT: B 20 MET cc_start: 0.6926 (pmm) cc_final: 0.6465 (pmm) REVERT: B 25 LYS cc_start: 0.7965 (pttt) cc_final: 0.7491 (pttt) REVERT: D 1 MET cc_start: 0.5230 (mmp) cc_final: 0.4524 (ttm) REVERT: D 29 GLN cc_start: 0.6082 (tt0) cc_final: 0.5870 (tm-30) REVERT: D 106 LYS cc_start: 0.7993 (mttt) cc_final: 0.7479 (mppt) REVERT: D 246 GLN cc_start: 0.7868 (pt0) cc_final: 0.7423 (tt0) REVERT: D 258 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7186 (tt0) outliers start: 30 outliers final: 13 residues processed: 134 average time/residue: 1.3135 time to fit residues: 186.2670 Evaluate side-chains 122 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 185 ASN 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 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 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.221994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.184150 restraints weight = 8272.815| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.05 r_work: 0.4088 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8004 Z= 0.185 Angle : 0.530 6.146 10892 Z= 0.274 Chirality : 0.045 0.137 1320 Planarity : 0.004 0.039 1412 Dihedral : 3.950 21.026 1126 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.13 % Allowed : 16.51 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 1036 helix: 2.03 (0.25), residues: 416 sheet: 0.64 (0.35), residues: 244 loop : 0.31 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 30 HIS 0.012 0.001 HIS A 87 PHE 0.009 0.001 PHE A 198 TYR 0.008 0.001 TYR D 120 ARG 0.008 0.000 ARG C 57 *********************** 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 153 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7414 (mp0) cc_final: 0.7008 (mp0) REVERT: A 75 ARG cc_start: 0.6702 (tpp-160) cc_final: 0.6442 (tpm170) REVERT: A 124 ARG cc_start: 0.6129 (mmt180) cc_final: 0.5754 (mpt-90) REVERT: A 246 GLN cc_start: 0.6584 (pt0) cc_final: 0.6091 (tt0) REVERT: B 20 MET cc_start: 0.6940 (pmm) cc_final: 0.6468 (pmm) REVERT: B 25 LYS cc_start: 0.7976 (pttt) cc_final: 0.7485 (pttt) REVERT: B 121 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7199 (m-30) REVERT: B 175 LEU cc_start: 0.6983 (tp) cc_final: 0.6713 (mm) REVERT: B 237 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: D 1 MET cc_start: 0.5424 (mmp) cc_final: 0.4698 (ttm) REVERT: D 29 GLN cc_start: 0.6062 (tt0) cc_final: 0.5826 (tm-30) REVERT: D 106 LYS cc_start: 0.8073 (mttt) cc_final: 0.7603 (mppt) REVERT: D 246 GLN cc_start: 0.7930 (pt0) cc_final: 0.7494 (tt0) REVERT: D 258 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7242 (tt0) outliers start: 35 outliers final: 17 residues processed: 137 average time/residue: 1.5626 time to fit residues: 225.4840 Evaluate side-chains 120 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 144 LYS Chi-restraints excluded: chain B residue 185 ASN 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 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 214 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 27 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.218210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.178944 restraints weight = 8206.375| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.10 r_work: 0.4015 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8004 Z= 0.253 Angle : 0.578 7.653 10892 Z= 0.299 Chirality : 0.047 0.143 1320 Planarity : 0.004 0.035 1412 Dihedral : 4.138 19.840 1126 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.13 % Allowed : 18.04 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1036 helix: 1.91 (0.25), residues: 416 sheet: 0.47 (0.34), residues: 244 loop : 0.29 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 30 HIS 0.004 0.001 HIS D 243 PHE 0.013 0.002 PHE B 198 TYR 0.009 0.001 TYR D 120 ARG 0.010 0.001 ARG C 57 *********************** 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 143 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.277 Fit side-chains REVERT: A 56 GLU cc_start: 0.7487 (mp0) cc_final: 0.7025 (mp0) REVERT: A 124 ARG cc_start: 0.6197 (mmt180) cc_final: 0.5850 (mpt-90) REVERT: A 246 GLN cc_start: 0.6570 (pt0) cc_final: 0.6075 (tt0) REVERT: A 260 ASN cc_start: 0.5392 (OUTLIER) cc_final: 0.5072 (m-40) REVERT: B 20 MET cc_start: 0.6936 (pmm) cc_final: 0.6472 (pmm) REVERT: B 25 LYS cc_start: 0.8053 (pttt) cc_final: 0.7525 (pttt) REVERT: B 121 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7416 (t70) REVERT: B 175 LEU cc_start: 0.7068 (tp) cc_final: 0.6792 (mm) REVERT: B 237 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: C 57 ARG cc_start: 0.6971 (ttp-110) cc_final: 0.6378 (mtm180) REVERT: D 1 MET cc_start: 0.5321 (mmp) cc_final: 0.4570 (ttm) REVERT: D 29 GLN cc_start: 0.6287 (tt0) cc_final: 0.5934 (tm-30) REVERT: D 106 LYS cc_start: 0.8081 (mttt) cc_final: 0.7570 (mppt) REVERT: D 246 GLN cc_start: 0.7899 (pt0) cc_final: 0.7441 (tt0) REVERT: D 258 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7271 (tt0) outliers start: 35 outliers final: 21 residues processed: 129 average time/residue: 1.4710 time to fit residues: 200.0644 Evaluate side-chains 125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL 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 121 ASP Chi-restraints excluded: chain B residue 139 ASP 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 36 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 61 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 0.0570 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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 247 HIS B 260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.220457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.181860 restraints weight = 8169.845| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.09 r_work: 0.4053 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8004 Z= 0.190 Angle : 0.547 10.695 10892 Z= 0.279 Chirality : 0.045 0.137 1320 Planarity : 0.004 0.037 1412 Dihedral : 3.869 16.765 1124 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.25 % Allowed : 19.34 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.27), residues: 1036 helix: 2.11 (0.26), residues: 416 sheet: 0.44 (0.34), residues: 248 loop : 0.32 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 30 HIS 0.004 0.001 HIS A 87 PHE 0.009 0.001 PHE A 198 TYR 0.008 0.001 TYR D 120 ARG 0.013 0.000 ARG D 57 *********************** 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 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7571 (mp0) cc_final: 0.7125 (mp0) REVERT: A 124 ARG cc_start: 0.6151 (mmt180) cc_final: 0.5833 (mpt-90) REVERT: A 246 GLN cc_start: 0.6473 (pt0) cc_final: 0.5957 (tt0) REVERT: A 260 ASN cc_start: 0.5314 (OUTLIER) cc_final: 0.4990 (m-40) REVERT: B 20 MET cc_start: 0.6925 (pmm) cc_final: 0.6469 (pmm) REVERT: B 25 LYS cc_start: 0.8036 (pttt) cc_final: 0.7515 (pttt) REVERT: B 121 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7374 (t70) REVERT: B 175 LEU cc_start: 0.7090 (tp) cc_final: 0.6812 (mm) REVERT: B 237 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: D 1 MET cc_start: 0.5396 (mmp) cc_final: 0.4666 (ttm) REVERT: D 29 GLN cc_start: 0.6141 (tt0) cc_final: 0.5849 (tm-30) REVERT: D 106 LYS cc_start: 0.8070 (mttt) cc_final: 0.7564 (mppt) REVERT: D 246 GLN cc_start: 0.7778 (pt0) cc_final: 0.7349 (tt0) REVERT: D 259 ARG cc_start: 0.6636 (ttm110) cc_final: 0.5900 (ptp90) outliers start: 36 outliers final: 20 residues processed: 134 average time/residue: 1.4019 time to fit residues: 197.7597 Evaluate side-chains 132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 104 ASN Chi-restraints excluded: chain B residue 121 ASP 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 82 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL 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 134 SER 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 36 optimal weight: 0.0370 chunk 102 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 10 optimal weight: 0.3980 chunk 86 optimal weight: 0.0370 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 B 185 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 = 0.4556 r_free = 0.4556 target = 0.222409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.184647 restraints weight = 8165.609| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.06 r_work: 0.4078 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8004 Z= 0.168 Angle : 0.556 11.989 10892 Z= 0.279 Chirality : 0.044 0.134 1320 Planarity : 0.004 0.046 1412 Dihedral : 3.727 16.664 1124 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.30 % Allowed : 20.87 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.27), residues: 1036 helix: 2.31 (0.26), residues: 412 sheet: 0.44 (0.34), residues: 248 loop : 0.36 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 30 HIS 0.004 0.000 HIS A 87 PHE 0.009 0.001 PHE A 198 TYR 0.011 0.001 TYR A 81 ARG 0.012 0.000 ARG C 57 *********************** 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 141 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7574 (mp0) cc_final: 0.7222 (mp0) REVERT: A 124 ARG cc_start: 0.6138 (mmt180) cc_final: 0.5853 (mpt-90) REVERT: A 246 GLN cc_start: 0.6494 (pt0) cc_final: 0.5973 (tt0) REVERT: A 260 ASN cc_start: 0.5263 (OUTLIER) cc_final: 0.4913 (m-40) REVERT: B 20 MET cc_start: 0.6935 (pmm) cc_final: 0.6477 (pmm) REVERT: B 25 LYS cc_start: 0.8031 (pttt) cc_final: 0.7525 (pttt) REVERT: B 102 VAL cc_start: 0.6736 (t) cc_final: 0.6306 (m) REVERT: B 121 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7382 (t70) REVERT: B 175 LEU cc_start: 0.7060 (tp) cc_final: 0.6748 (mm) REVERT: B 237 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7214 (mm-30) REVERT: C 57 ARG cc_start: 0.6939 (ttp-110) cc_final: 0.6369 (mtm180) REVERT: D 1 MET cc_start: 0.5376 (mmp) cc_final: 0.4696 (ttm) REVERT: D 29 GLN cc_start: 0.6055 (tt0) cc_final: 0.5800 (tm-30) REVERT: D 91 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5807 (mt-10) REVERT: D 106 LYS cc_start: 0.8078 (mttt) cc_final: 0.7575 (mppt) REVERT: D 246 GLN cc_start: 0.7767 (pt0) cc_final: 0.7355 (tt0) REVERT: D 259 ARG cc_start: 0.6607 (ttm110) cc_final: 0.5894 (ptp90) outliers start: 28 outliers final: 14 residues processed: 129 average time/residue: 1.7254 time to fit residues: 233.9229 Evaluate side-chains 127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 121 ASP 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 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 91 GLU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 175 LEU 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 79 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN D 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.217981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.180081 restraints weight = 8239.693| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.11 r_work: 0.4022 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8004 Z= 0.263 Angle : 0.620 12.878 10892 Z= 0.315 Chirality : 0.047 0.139 1320 Planarity : 0.004 0.050 1412 Dihedral : 4.043 16.222 1124 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.48 % Allowed : 20.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 1036 helix: 2.09 (0.26), residues: 412 sheet: 0.31 (0.33), residues: 248 loop : 0.32 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.005 0.001 HIS D 243 PHE 0.014 0.002 PHE B 198 TYR 0.012 0.001 TYR A 81 ARG 0.012 0.001 ARG D 57 *********************** 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 147 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7593 (mp0) cc_final: 0.7218 (mp0) REVERT: A 124 ARG cc_start: 0.6069 (mmt180) cc_final: 0.5796 (mpt-90) REVERT: A 246 GLN cc_start: 0.6441 (pt0) cc_final: 0.5975 (tt0) REVERT: A 260 ASN cc_start: 0.5291 (OUTLIER) cc_final: 0.4926 (m-40) REVERT: B 20 MET cc_start: 0.6885 (pmm) cc_final: 0.6439 (pmm) REVERT: B 25 LYS cc_start: 0.8018 (pttt) cc_final: 0.7496 (pttt) REVERT: B 102 VAL cc_start: 0.7054 (OUTLIER) cc_final: 0.6588 (m) REVERT: B 121 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7364 (t70) REVERT: B 175 LEU cc_start: 0.7116 (tp) cc_final: 0.6822 (mm) REVERT: B 237 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: C 22 GLU cc_start: 0.7384 (tp30) cc_final: 0.7039 (tp30) REVERT: C 25 LYS cc_start: 0.7937 (mptt) cc_final: 0.7706 (mtmt) REVERT: C 57 ARG cc_start: 0.7034 (ttp-110) cc_final: 0.6381 (mtm180) REVERT: C 160 SER cc_start: 0.4067 (OUTLIER) cc_final: 0.3318 (m) REVERT: C 224 ILE cc_start: 0.8112 (mt) cc_final: 0.7598 (mm) REVERT: D 1 MET cc_start: 0.5397 (mmp) cc_final: 0.4654 (ttm) REVERT: D 29 GLN cc_start: 0.6296 (tt0) cc_final: 0.5940 (tm-30) REVERT: D 33 ARG cc_start: 0.7813 (mtt-85) cc_final: 0.7500 (mpt180) REVERT: D 106 LYS cc_start: 0.8132 (mttt) cc_final: 0.7639 (mppt) REVERT: D 246 GLN cc_start: 0.7821 (pt0) cc_final: 0.7406 (tt0) REVERT: D 259 ARG cc_start: 0.6622 (ttm110) cc_final: 0.5890 (ptp90) outliers start: 38 outliers final: 24 residues processed: 132 average time/residue: 1.9045 time to fit residues: 263.8696 Evaluate side-chains 138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 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 121 ASP Chi-restraints excluded: chain B residue 139 ASP 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 102 VAL Chi-restraints excluded: chain C residue 160 SER 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 134 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN D 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.214290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.175743 restraints weight = 8343.072| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.24 r_work: 0.3958 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8004 Z= 0.385 Angle : 0.700 14.067 10892 Z= 0.360 Chirality : 0.050 0.182 1320 Planarity : 0.005 0.049 1412 Dihedral : 4.474 16.636 1124 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.48 % Allowed : 21.11 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1036 helix: 1.60 (0.25), residues: 412 sheet: 0.11 (0.33), residues: 248 loop : 0.16 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.007 0.001 HIS D 243 PHE 0.018 0.002 PHE B 198 TYR 0.012 0.002 TYR D 120 ARG 0.012 0.001 ARG D 57 *********************** 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 144 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.849 Fit side-chains REVERT: A 56 GLU cc_start: 0.7520 (mp0) cc_final: 0.7132 (mp0) REVERT: A 166 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6075 (ttp80) REVERT: A 246 GLN cc_start: 0.6515 (pt0) cc_final: 0.6059 (tt0) REVERT: A 260 ASN cc_start: 0.5406 (OUTLIER) cc_final: 0.5035 (m-40) REVERT: B 20 MET cc_start: 0.6877 (pmm) cc_final: 0.6132 (pmm) REVERT: B 23 HIS cc_start: 0.6792 (m90) cc_final: 0.6557 (m90) REVERT: B 25 LYS cc_start: 0.8048 (pttt) cc_final: 0.7604 (ptmt) REVERT: B 175 LEU cc_start: 0.7224 (tp) cc_final: 0.6967 (mm) REVERT: B 237 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7257 (mm-30) REVERT: C 22 GLU cc_start: 0.7453 (tp30) cc_final: 0.7183 (tp30) REVERT: C 224 ILE cc_start: 0.8166 (mt) cc_final: 0.7677 (mm) REVERT: D 1 MET cc_start: 0.5498 (mmp) cc_final: 0.4702 (ttm) REVERT: D 29 GLN cc_start: 0.6370 (tt0) cc_final: 0.5964 (tm-30) REVERT: D 33 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7560 (mpt180) REVERT: D 106 LYS cc_start: 0.8262 (mttt) cc_final: 0.7715 (mppt) REVERT: D 224 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8248 (mm) REVERT: D 246 GLN cc_start: 0.7933 (pt0) cc_final: 0.7511 (tt0) REVERT: D 259 ARG cc_start: 0.6645 (ttm110) cc_final: 0.5912 (ptp90) outliers start: 38 outliers final: 26 residues processed: 129 average time/residue: 1.2978 time to fit residues: 176.9882 Evaluate side-chains 133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 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 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 224 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 0.0070 chunk 74 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.221233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.182096 restraints weight = 8255.602| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.11 r_work: 0.4058 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8004 Z= 0.186 Angle : 0.606 14.411 10892 Z= 0.301 Chirality : 0.045 0.141 1320 Planarity : 0.004 0.054 1412 Dihedral : 3.875 17.151 1124 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.30 % Allowed : 21.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 1036 helix: 2.10 (0.26), residues: 408 sheet: 0.24 (0.34), residues: 248 loop : 0.37 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 30 HIS 0.002 0.000 HIS D 72 PHE 0.007 0.001 PHE B 198 TYR 0.014 0.001 TYR A 81 ARG 0.016 0.000 ARG C 57 *********************** 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 135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7523 (mp0) cc_final: 0.7154 (mp0) REVERT: A 246 GLN cc_start: 0.6440 (pt0) cc_final: 0.5884 (tt0) REVERT: B 20 MET cc_start: 0.6870 (pmm) cc_final: 0.6136 (pmm) REVERT: B 23 HIS cc_start: 0.6678 (m90) cc_final: 0.6432 (m90) REVERT: B 25 LYS cc_start: 0.8007 (pttt) cc_final: 0.7576 (ptmt) REVERT: B 102 VAL cc_start: 0.6863 (t) cc_final: 0.6440 (m) REVERT: B 175 LEU cc_start: 0.7143 (tp) cc_final: 0.6819 (mm) REVERT: B 237 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: C 25 LYS cc_start: 0.8472 (mtmt) cc_final: 0.8059 (mmmt) REVERT: C 57 ARG cc_start: 0.6991 (ttp-110) cc_final: 0.6429 (mtm180) REVERT: D 1 MET cc_start: 0.5467 (mmp) cc_final: 0.4773 (ttm) REVERT: D 29 GLN cc_start: 0.6157 (tt0) cc_final: 0.5849 (tm-30) REVERT: D 53 GLU cc_start: 0.7520 (pm20) cc_final: 0.7262 (pt0) REVERT: D 106 LYS cc_start: 0.8166 (mttt) cc_final: 0.7677 (mppt) REVERT: D 246 GLN cc_start: 0.7745 (pt0) cc_final: 0.7355 (tt0) REVERT: D 259 ARG cc_start: 0.6496 (ttm110) cc_final: 0.5792 (ptp90) outliers start: 28 outliers final: 16 residues processed: 122 average time/residue: 1.3163 time to fit residues: 169.3259 Evaluate side-chains 123 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 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 D residue 36 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 0.0970 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.4506 r_free = 0.4506 target = 0.216515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.178707 restraints weight = 8201.673| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.18 r_work: 0.3992 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8004 Z= 0.296 Angle : 0.668 14.713 10892 Z= 0.337 Chirality : 0.048 0.161 1320 Planarity : 0.005 0.055 1412 Dihedral : 4.179 16.542 1124 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.83 % Allowed : 23.00 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1036 helix: 1.85 (0.26), residues: 408 sheet: 0.12 (0.33), residues: 248 loop : 0.31 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.005 0.001 HIS D 243 PHE 0.016 0.002 PHE B 198 TYR 0.021 0.002 TYR A 81 ARG 0.014 0.001 ARG C 57 ********************** 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 130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7511 (mp0) cc_final: 0.7198 (mp0) REVERT: A 246 GLN cc_start: 0.6442 (pt0) cc_final: 0.5952 (tt0) REVERT: B 20 MET cc_start: 0.6911 (pmm) cc_final: 0.6186 (pmm) REVERT: B 23 HIS cc_start: 0.6773 (m90) cc_final: 0.6546 (m90) REVERT: B 25 LYS cc_start: 0.8031 (pttt) cc_final: 0.7591 (ptmt) REVERT: B 175 LEU cc_start: 0.7210 (tp) cc_final: 0.6919 (mm) REVERT: B 237 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: C 25 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8062 (mptp) REVERT: C 57 ARG cc_start: 0.7117 (ttp-110) cc_final: 0.6363 (mtm180) REVERT: D 1 MET cc_start: 0.5432 (mmp) cc_final: 0.4699 (ttm) REVERT: D 29 GLN cc_start: 0.6370 (tt0) cc_final: 0.5998 (tm-30) REVERT: D 33 ARG cc_start: 0.7859 (mtt-85) cc_final: 0.7487 (mpt180) REVERT: D 106 LYS cc_start: 0.8284 (mttt) cc_final: 0.7738 (mppt) REVERT: D 246 GLN cc_start: 0.7815 (pt0) cc_final: 0.7416 (tt0) REVERT: D 259 ARG cc_start: 0.6586 (ttm110) cc_final: 0.5875 (ptp90) outliers start: 24 outliers final: 19 residues processed: 123 average time/residue: 1.3292 time to fit residues: 172.3207 Evaluate side-chains 124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 B residue 104 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 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 D residue 36 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.214043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.175679 restraints weight = 8312.054| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.21 r_work: 0.3960 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8004 Z= 0.372 Angle : 0.721 15.200 10892 Z= 0.367 Chirality : 0.050 0.191 1320 Planarity : 0.005 0.047 1412 Dihedral : 4.482 16.723 1124 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.54 % Allowed : 22.64 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1036 helix: 1.49 (0.25), residues: 408 sheet: -0.12 (0.33), residues: 252 loop : 0.21 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 82 HIS 0.006 0.001 HIS D 243 PHE 0.018 0.002 PHE B 198 TYR 0.014 0.002 TYR A 81 ARG 0.014 0.001 ARG C 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7457.21 seconds wall clock time: 131 minutes 23.62 seconds (7883.62 seconds total)