Starting phenix.real_space_refine on Sat Dec 28 04:49:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b79_44304/12_2024/9b79_44304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b79_44304/12_2024/9b79_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_44304/12_2024/9b79_44304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b79_44304/12_2024/9b79_44304.map" model { file = "/net/cci-nas-00/data/ceres_data/9b79_44304/12_2024/9b79_44304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b79_44304/12_2024/9b79_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-5532/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: 5.13, per 1000 atoms: 0.65 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: 1.96 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: 0.91 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: 2.30 Time building geometry restraints manager: 2.25 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: 0.00 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: 0.960 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.390 Find NCS groups from input model: 0.250 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- 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 : 0.910 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: 1.4155 time to fit residues: 260.0874 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 : 0.966 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1625 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 6.068 10892 Z= 0.291 Chirality : 0.046 0.143 1320 Planarity : 0.004 0.033 1412 Dihedral : 4.105 21.442 1126 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.42 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 : 0.934 Fit side-chains REVERT: A 25 LYS cc_start: 0.7459 (pttt) cc_final: 0.7248 (tptt) REVERT: A 56 GLU cc_start: 0.7509 (mp0) cc_final: 0.7103 (mp0) REVERT: A 89 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4662 (tp) REVERT: A 90 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6447 (pp) REVERT: A 124 ARG cc_start: 0.6108 (mmt180) cc_final: 0.5820 (mpt-90) REVERT: A 246 GLN cc_start: 0.6619 (pt0) cc_final: 0.6145 (tt0) REVERT: B 20 MET cc_start: 0.6447 (pmm) cc_final: 0.5924 (pmm) REVERT: B 25 LYS cc_start: 0.7360 (pttt) cc_final: 0.6707 (pttt) REVERT: B 48 ASP cc_start: 0.6185 (t0) cc_final: 0.5926 (m-30) REVERT: B 142 SER cc_start: 0.8133 (m) cc_final: 0.7858 (p) REVERT: D 1 MET cc_start: 0.4435 (mmp) cc_final: 0.3574 (ttm) REVERT: D 25 LYS cc_start: 0.7519 (pttt) cc_final: 0.7169 (ptmt) REVERT: D 29 GLN cc_start: 0.6154 (tt0) cc_final: 0.5847 (tm-30) REVERT: D 106 LYS cc_start: 0.7282 (mttt) cc_final: 0.6480 (mppt) REVERT: D 246 GLN cc_start: 0.7635 (pt0) cc_final: 0.7150 (tt0) REVERT: D 258 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6557 (tt0) outliers start: 30 outliers final: 13 residues processed: 134 average time/residue: 1.3731 time to fit residues: 194.7891 Evaluate side-chains 124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 52 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1938 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= 0.253 Angle : 0.570 5.960 10892 Z= 0.297 Chirality : 0.046 0.141 1320 Planarity : 0.004 0.043 1412 Dihedral : 4.170 20.975 1126 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.60 % Allowed : 15.92 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.26), residues: 1036 helix: 1.84 (0.25), residues: 416 sheet: 0.95 (0.35), residues: 228 loop : 0.10 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 30 HIS 0.011 0.001 HIS A 87 PHE 0.012 0.002 PHE B 198 TYR 0.009 0.001 TYR D 120 ARG 0.007 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 155 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.953 Fit side-chains REVERT: A 25 LYS cc_start: 0.7443 (pttt) cc_final: 0.7190 (tptt) REVERT: A 56 GLU cc_start: 0.7566 (mp0) cc_final: 0.7170 (mp0) REVERT: A 90 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6407 (pp) REVERT: A 124 ARG cc_start: 0.6184 (mmt180) cc_final: 0.5824 (mpt-90) REVERT: A 166 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.6365 (ttp80) REVERT: A 246 GLN cc_start: 0.6685 (pt0) cc_final: 0.6214 (tt0) REVERT: B 20 MET cc_start: 0.6460 (pmm) cc_final: 0.5934 (pmm) REVERT: B 25 LYS cc_start: 0.7345 (pttt) cc_final: 0.6662 (pttt) REVERT: B 29 GLN cc_start: 0.6551 (tt0) cc_final: 0.6313 (tt0) REVERT: B 48 ASP cc_start: 0.6152 (t0) cc_final: 0.5904 (m-30) REVERT: B 142 SER cc_start: 0.8173 (m) cc_final: 0.7860 (p) REVERT: B 237 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7130 (mm-30) REVERT: D 1 MET cc_start: 0.4411 (mmp) cc_final: 0.3481 (ttm) REVERT: D 25 LYS cc_start: 0.7581 (pttt) cc_final: 0.7206 (ptmt) REVERT: D 29 GLN cc_start: 0.6225 (tt0) cc_final: 0.5850 (tm-30) REVERT: D 106 LYS cc_start: 0.7317 (mttt) cc_final: 0.6470 (mppt) REVERT: D 224 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8064 (mm) REVERT: D 246 GLN cc_start: 0.7665 (pt0) cc_final: 0.7193 (tt0) REVERT: D 251 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7269 (tp-100) REVERT: D 258 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6523 (tt0) outliers start: 39 outliers final: 20 residues processed: 141 average time/residue: 1.3114 time to fit residues: 195.4002 Evaluate side-chains 129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 90 ILE 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 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 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 Chi-restraints excluded: chain D residue 224 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8004 Z= 0.179 Angle : 0.533 7.437 10892 Z= 0.273 Chirality : 0.045 0.139 1320 Planarity : 0.004 0.032 1412 Dihedral : 3.858 16.901 1124 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.42 % Allowed : 18.28 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1036 helix: 2.07 (0.26), residues: 416 sheet: 0.55 (0.34), residues: 244 loop : 0.36 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 30 HIS 0.003 0.000 HIS A 87 PHE 0.009 0.001 PHE A 198 TYR 0.007 0.001 TYR D 120 ARG 0.009 0.000 ARG D 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 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7355 (pttt) cc_final: 0.7081 (tptt) REVERT: A 56 GLU cc_start: 0.7650 (mp0) cc_final: 0.7278 (mp0) REVERT: A 124 ARG cc_start: 0.6153 (mmt180) cc_final: 0.5898 (mpt-90) REVERT: A 246 GLN cc_start: 0.6593 (pt0) cc_final: 0.6099 (tt0) REVERT: A 260 ASN cc_start: 0.5280 (OUTLIER) cc_final: 0.5005 (m-40) REVERT: B 20 MET cc_start: 0.6408 (pmm) cc_final: 0.5900 (pmm) REVERT: B 25 LYS cc_start: 0.7466 (pttt) cc_final: 0.6784 (pttt) REVERT: B 48 ASP cc_start: 0.6157 (t0) cc_final: 0.5859 (m-30) REVERT: B 142 SER cc_start: 0.8228 (m) cc_final: 0.7935 (p) REVERT: B 237 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: D 1 MET cc_start: 0.4545 (mmp) cc_final: 0.3672 (ttm) REVERT: D 25 LYS cc_start: 0.7622 (pttt) cc_final: 0.7224 (ptmt) REVERT: D 29 GLN cc_start: 0.6133 (tt0) cc_final: 0.5799 (tm-30) REVERT: D 106 LYS cc_start: 0.7366 (mttt) cc_final: 0.6523 (mppt) REVERT: D 246 GLN cc_start: 0.7590 (pt0) cc_final: 0.7154 (tt0) REVERT: D 258 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6596 (tt0) REVERT: D 259 ARG cc_start: 0.6097 (ttm110) cc_final: 0.5269 (ptp90) outliers start: 29 outliers final: 18 residues processed: 133 average time/residue: 1.5059 time to fit residues: 210.1482 Evaluate side-chains 125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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 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 57 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 D 251 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8004 Z= 0.398 Angle : 0.681 10.352 10892 Z= 0.352 Chirality : 0.050 0.160 1320 Planarity : 0.005 0.035 1412 Dihedral : 4.489 16.447 1124 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.83 % Allowed : 18.75 % 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: 1.04 (0.26), residues: 1036 helix: 1.50 (0.25), residues: 416 sheet: 0.56 (0.34), residues: 232 loop : 0.00 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.009 0.001 HIS D 243 PHE 0.018 0.002 PHE B 198 TYR 0.012 0.002 TYR D 120 ARG 0.013 0.001 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 146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7684 (mp0) cc_final: 0.7370 (mp0) REVERT: A 246 GLN cc_start: 0.6627 (pt0) cc_final: 0.6185 (tt0) REVERT: A 259 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7655 (mtp85) REVERT: A 260 ASN cc_start: 0.5328 (OUTLIER) cc_final: 0.5052 (m-40) REVERT: B 20 MET cc_start: 0.6385 (pmm) cc_final: 0.5583 (pmm) REVERT: B 23 HIS cc_start: 0.6253 (m90) cc_final: 0.5967 (m90) REVERT: B 25 LYS cc_start: 0.7408 (pttt) cc_final: 0.6750 (ptmt) REVERT: B 48 ASP cc_start: 0.6255 (t0) cc_final: 0.5954 (m-30) REVERT: B 142 SER cc_start: 0.8129 (m) cc_final: 0.7751 (p) REVERT: B 237 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7144 (mm-30) REVERT: C 57 ARG cc_start: 0.7026 (ttp-110) cc_final: 0.6414 (mtm180) REVERT: D 1 MET cc_start: 0.4531 (mmp) cc_final: 0.3587 (ttm) REVERT: D 25 LYS cc_start: 0.7684 (pttt) cc_final: 0.7341 (ptmt) REVERT: D 29 GLN cc_start: 0.6349 (tt0) cc_final: 0.5913 (tm-30) REVERT: D 106 LYS cc_start: 0.7355 (mttt) cc_final: 0.6515 (mppt) REVERT: D 246 GLN cc_start: 0.7653 (pt0) cc_final: 0.7172 (tt0) outliers start: 41 outliers final: 23 residues processed: 132 average time/residue: 1.5262 time to fit residues: 211.9696 Evaluate side-chains 132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS D 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8004 Z= 0.262 Angle : 0.613 9.504 10892 Z= 0.313 Chirality : 0.047 0.170 1320 Planarity : 0.004 0.043 1412 Dihedral : 4.225 17.072 1124 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.48 % Allowed : 19.81 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1036 helix: 1.76 (0.25), residues: 416 sheet: 0.56 (0.34), residues: 232 loop : 0.06 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.004 0.001 HIS A 87 PHE 0.011 0.001 PHE B 198 TYR 0.010 0.001 TYR D 120 ARG 0.012 0.001 ARG D 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 146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7465 (pttt) cc_final: 0.7192 (tptt) REVERT: A 56 GLU cc_start: 0.7700 (mp0) cc_final: 0.7324 (mp0) REVERT: A 246 GLN cc_start: 0.6575 (pt0) cc_final: 0.6121 (tt0) REVERT: A 260 ASN cc_start: 0.5280 (OUTLIER) cc_final: 0.4999 (m-40) REVERT: B 20 MET cc_start: 0.6358 (pmm) cc_final: 0.5581 (pmm) REVERT: B 23 HIS cc_start: 0.6237 (m90) cc_final: 0.5947 (m90) REVERT: B 25 LYS cc_start: 0.7426 (pttt) cc_final: 0.6786 (ptmt) REVERT: B 48 ASP cc_start: 0.6227 (t0) cc_final: 0.5944 (m-30) REVERT: B 142 SER cc_start: 0.8077 (m) cc_final: 0.7740 (p) REVERT: B 237 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: B 260 ASN cc_start: 0.6867 (m110) cc_final: 0.6643 (m-40) REVERT: D 1 MET cc_start: 0.4532 (mmp) cc_final: 0.3661 (ttm) REVERT: D 25 LYS cc_start: 0.7679 (pttt) cc_final: 0.7333 (ptmt) REVERT: D 29 GLN cc_start: 0.6365 (tt0) cc_final: 0.5917 (tm-30) REVERT: D 106 LYS cc_start: 0.7368 (mttt) cc_final: 0.6530 (mppt) REVERT: D 246 GLN cc_start: 0.7556 (pt0) cc_final: 0.7122 (tt0) REVERT: D 259 ARG cc_start: 0.6124 (ttm110) cc_final: 0.5271 (ptp90) outliers start: 38 outliers final: 25 residues processed: 134 average time/residue: 1.3674 time to fit residues: 193.3680 Evaluate side-chains 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 172 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 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 90 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 0.0010 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.0020 chunk 59 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8004 Z= 0.175 Angle : 0.583 13.145 10892 Z= 0.291 Chirality : 0.045 0.141 1320 Planarity : 0.004 0.050 1412 Dihedral : 3.824 17.121 1124 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.66 % Allowed : 20.99 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1036 helix: 2.19 (0.26), residues: 412 sheet: 0.30 (0.34), residues: 248 loop : 0.30 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 30 HIS 0.003 0.000 HIS A 87 PHE 0.009 0.001 PHE A 198 TYR 0.008 0.001 TYR C 81 ARG 0.013 0.000 ARG C 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 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7436 (pttt) cc_final: 0.7066 (tptt) REVERT: A 56 GLU cc_start: 0.7665 (mp0) cc_final: 0.7338 (mp0) REVERT: A 246 GLN cc_start: 0.6543 (pt0) cc_final: 0.6029 (tt0) REVERT: A 260 ASN cc_start: 0.5332 (OUTLIER) cc_final: 0.5012 (m-40) REVERT: B 20 MET cc_start: 0.6283 (pmm) cc_final: 0.5795 (pmm) REVERT: B 25 LYS cc_start: 0.7465 (pttt) cc_final: 0.6782 (pttt) REVERT: B 48 ASP cc_start: 0.6187 (t0) cc_final: 0.5858 (m-30) REVERT: B 102 VAL cc_start: 0.5564 (OUTLIER) cc_final: 0.5328 (m) REVERT: B 142 SER cc_start: 0.8200 (m) cc_final: 0.7923 (p) REVERT: B 237 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: B 260 ASN cc_start: 0.6728 (m110) cc_final: 0.6492 (m-40) REVERT: C 22 GLU cc_start: 0.7425 (tp30) cc_final: 0.7164 (tp30) REVERT: C 25 LYS cc_start: 0.7974 (mptt) cc_final: 0.7748 (mtmt) REVERT: C 57 ARG cc_start: 0.7012 (ttp-110) cc_final: 0.6436 (mtm180) REVERT: D 1 MET cc_start: 0.4510 (mmp) cc_final: 0.3731 (ttm) REVERT: D 25 LYS cc_start: 0.7627 (pttt) cc_final: 0.7278 (ptmt) REVERT: D 29 GLN cc_start: 0.6195 (tt0) cc_final: 0.5784 (tm-30) REVERT: D 106 LYS cc_start: 0.7369 (mttt) cc_final: 0.6558 (mppt) REVERT: D 179 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6828 (mtp-110) REVERT: D 246 GLN cc_start: 0.7518 (pt0) cc_final: 0.7108 (tt0) REVERT: D 259 ARG cc_start: 0.6079 (ttm110) cc_final: 0.5202 (ptp90) outliers start: 31 outliers final: 17 residues processed: 132 average time/residue: 1.3376 time to fit residues: 186.3474 Evaluate side-chains 126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 172 ARG Chi-restraints excluded: chain A residue 260 ASN 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 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 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 D residue 36 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 0.0770 chunk 93 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2526 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= 0.231 Angle : 0.618 13.929 10892 Z= 0.311 Chirality : 0.046 0.138 1320 Planarity : 0.004 0.043 1412 Dihedral : 3.965 16.609 1124 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.25 % Allowed : 21.11 % Favored : 74.65 % 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: 2.11 (0.26), residues: 412 sheet: 0.28 (0.34), residues: 248 loop : 0.31 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 30 HIS 0.004 0.001 HIS D 72 PHE 0.012 0.001 PHE B 198 TYR 0.012 0.001 TYR A 81 ARG 0.011 0.000 ARG C 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 147 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7425 (pttt) cc_final: 0.7111 (tptt) REVERT: A 56 GLU cc_start: 0.7669 (mp0) cc_final: 0.7289 (mp0) REVERT: A 246 GLN cc_start: 0.6545 (pt0) cc_final: 0.6069 (tt0) REVERT: A 260 ASN cc_start: 0.5233 (OUTLIER) cc_final: 0.4916 (m-40) REVERT: B 20 MET cc_start: 0.6345 (pmm) cc_final: 0.5568 (pmm) REVERT: B 23 HIS cc_start: 0.6296 (m90) cc_final: 0.6017 (m90) REVERT: B 25 LYS cc_start: 0.7426 (pttt) cc_final: 0.6793 (ptmt) REVERT: B 48 ASP cc_start: 0.6147 (t0) cc_final: 0.5848 (m-30) REVERT: B 102 VAL cc_start: 0.5785 (OUTLIER) cc_final: 0.5535 (m) REVERT: B 142 SER cc_start: 0.8208 (m) cc_final: 0.7898 (p) REVERT: B 237 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7142 (mm-30) REVERT: B 260 ASN cc_start: 0.6776 (m110) cc_final: 0.6535 (m-40) REVERT: C 57 ARG cc_start: 0.7110 (ttp-110) cc_final: 0.6448 (mtm180) REVERT: C 224 ILE cc_start: 0.8112 (mt) cc_final: 0.7605 (mm) REVERT: D 1 MET cc_start: 0.4508 (mmp) cc_final: 0.3693 (ttm) REVERT: D 25 LYS cc_start: 0.7685 (pttt) cc_final: 0.7379 (ptmt) REVERT: D 29 GLN cc_start: 0.6329 (tt0) cc_final: 0.5912 (tm-30) REVERT: D 53 GLU cc_start: 0.7389 (pm20) cc_final: 0.7146 (pt0) REVERT: D 106 LYS cc_start: 0.7394 (mttt) cc_final: 0.6583 (mppt) REVERT: D 246 GLN cc_start: 0.7595 (pt0) cc_final: 0.7198 (tt0) REVERT: D 259 ARG cc_start: 0.6003 (ttm110) cc_final: 0.5149 (ptp90) outliers start: 36 outliers final: 26 residues processed: 132 average time/residue: 1.3903 time to fit residues: 193.5420 Evaluate side-chains 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 172 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain B residue 22 GLU 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 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 114 VAL 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 96 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8004 Z= 0.195 Angle : 0.614 14.929 10892 Z= 0.306 Chirality : 0.045 0.137 1320 Planarity : 0.004 0.053 1412 Dihedral : 3.851 17.058 1124 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.89 % Allowed : 21.93 % 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: 1.55 (0.27), residues: 1036 helix: 2.19 (0.26), residues: 408 sheet: 0.31 (0.34), residues: 248 loop : 0.37 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 30 HIS 0.003 0.000 HIS D 72 PHE 0.009 0.001 PHE A 198 TYR 0.008 0.001 TYR A 81 ARG 0.013 0.000 ARG D 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 139 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7438 (pttt) cc_final: 0.7063 (tptt) REVERT: A 56 GLU cc_start: 0.7662 (mp0) cc_final: 0.7327 (mp0) REVERT: A 121 ASP cc_start: 0.6903 (m-30) cc_final: 0.6505 (t0) REVERT: A 246 GLN cc_start: 0.6556 (pt0) cc_final: 0.6031 (tt0) REVERT: A 260 ASN cc_start: 0.5208 (OUTLIER) cc_final: 0.4909 (m-40) REVERT: B 20 MET cc_start: 0.6357 (pmm) cc_final: 0.5580 (pmm) REVERT: B 23 HIS cc_start: 0.6324 (m90) cc_final: 0.6042 (m90) REVERT: B 25 LYS cc_start: 0.7421 (pttt) cc_final: 0.6746 (pttt) REVERT: B 48 ASP cc_start: 0.6122 (t0) cc_final: 0.5833 (m-30) REVERT: B 102 VAL cc_start: 0.5570 (OUTLIER) cc_final: 0.5341 (m) REVERT: B 142 SER cc_start: 0.8194 (m) cc_final: 0.7916 (p) REVERT: B 237 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: B 260 ASN cc_start: 0.6823 (m110) cc_final: 0.6613 (m-40) REVERT: C 22 GLU cc_start: 0.7395 (tp30) cc_final: 0.7167 (tp30) REVERT: C 57 ARG cc_start: 0.7096 (ttp-110) cc_final: 0.6448 (mtm180) REVERT: C 224 ILE cc_start: 0.8054 (mt) cc_final: 0.7538 (mm) REVERT: D 1 MET cc_start: 0.4609 (mmp) cc_final: 0.3799 (ttm) REVERT: D 25 LYS cc_start: 0.7679 (pttt) cc_final: 0.7350 (ptmt) REVERT: D 29 GLN cc_start: 0.6214 (tt0) cc_final: 0.5854 (tm-30) REVERT: D 53 GLU cc_start: 0.7393 (pm20) cc_final: 0.7136 (pt0) REVERT: D 106 LYS cc_start: 0.7373 (mttt) cc_final: 0.6532 (mppt) REVERT: D 246 GLN cc_start: 0.7647 (pt0) cc_final: 0.7250 (tt0) REVERT: D 259 ARG cc_start: 0.5978 (ttm110) cc_final: 0.5132 (ptp90) outliers start: 33 outliers final: 23 residues processed: 125 average time/residue: 1.3074 time to fit residues: 172.7131 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 : 0.853 ------------------------------------------------------------------------------- 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 172 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ASN 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 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 114 VAL 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 46 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 0.0170 chunk 82 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 25 optimal weight: 8.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8004 Z= 0.256 Angle : 0.646 15.083 10892 Z= 0.324 Chirality : 0.047 0.308 1320 Planarity : 0.004 0.052 1412 Dihedral : 4.032 16.534 1124 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.77 % Allowed : 22.41 % 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: 1.38 (0.27), residues: 1036 helix: 2.04 (0.26), residues: 408 sheet: 0.13 (0.33), residues: 252 loop : 0.37 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.004 0.001 HIS D 72 PHE 0.014 0.002 PHE B 198 TYR 0.014 0.001 TYR A 81 ARG 0.013 0.001 ARG D 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 133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7437 (pttt) cc_final: 0.7111 (tptt) REVERT: A 56 GLU cc_start: 0.7636 (mp0) cc_final: 0.7258 (mp0) REVERT: A 246 GLN cc_start: 0.6545 (pt0) cc_final: 0.6052 (tt0) REVERT: A 260 ASN cc_start: 0.5257 (OUTLIER) cc_final: 0.4933 (m-40) REVERT: B 20 MET cc_start: 0.6361 (pmm) cc_final: 0.5559 (pmm) REVERT: B 23 HIS cc_start: 0.6400 (m90) cc_final: 0.6114 (m90) REVERT: B 25 LYS cc_start: 0.7431 (pttt) cc_final: 0.6798 (ptmt) REVERT: B 48 ASP cc_start: 0.6156 (t0) cc_final: 0.5851 (m-30) REVERT: B 102 VAL cc_start: 0.5835 (OUTLIER) cc_final: 0.5592 (m) REVERT: B 142 SER cc_start: 0.8209 (m) cc_final: 0.7887 (p) REVERT: B 237 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: B 260 ASN cc_start: 0.6804 (m110) cc_final: 0.6598 (m-40) REVERT: C 25 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8210 (mptp) REVERT: C 57 ARG cc_start: 0.7087 (ttp-110) cc_final: 0.6466 (mtm180) REVERT: C 224 ILE cc_start: 0.8050 (mt) cc_final: 0.7548 (mm) REVERT: D 1 MET cc_start: 0.4563 (mmp) cc_final: 0.3742 (ttm) REVERT: D 25 LYS cc_start: 0.7713 (pttt) cc_final: 0.7364 (ptmt) REVERT: D 29 GLN cc_start: 0.6362 (tt0) cc_final: 0.5947 (tm-30) REVERT: D 106 LYS cc_start: 0.7389 (mttt) cc_final: 0.6552 (mppt) REVERT: D 246 GLN cc_start: 0.7627 (pt0) cc_final: 0.7229 (tt0) REVERT: D 259 ARG cc_start: 0.6012 (ttm110) cc_final: 0.5173 (ptp90) outliers start: 32 outliers final: 24 residues processed: 121 average time/residue: 1.3024 time to fit residues: 166.5627 Evaluate side-chains 128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 225 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 239 HIS 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 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 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 76 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.0040 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.5396 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.216968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.178600 restraints weight = 8176.077| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.10 r_work: 0.4004 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8004 Z= 0.268 Angle : 0.654 15.009 10892 Z= 0.328 Chirality : 0.047 0.183 1320 Planarity : 0.004 0.045 1412 Dihedral : 4.100 16.609 1124 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.77 % Allowed : 22.41 % 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: 1.29 (0.27), residues: 1036 helix: 1.94 (0.26), residues: 408 sheet: 0.09 (0.33), residues: 252 loop : 0.34 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.004 0.001 HIS D 72 PHE 0.013 0.002 PHE B 198 TYR 0.023 0.002 TYR A 81 ARG 0.012 0.001 ARG D 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3514.72 seconds wall clock time: 63 minutes 49.37 seconds (3829.37 seconds total)