Starting phenix.real_space_refine on Sat May 10 10:47:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hry_34982/05_2025/8hry_34982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hry_34982/05_2025/8hry_34982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hry_34982/05_2025/8hry_34982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hry_34982/05_2025/8hry_34982.map" model { file = "/net/cci-nas-00/data/ceres_data/8hry_34982/05_2025/8hry_34982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hry_34982/05_2025/8hry_34982.cif" } resolution = 3.11 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3880 2.51 5 N 976 2.21 5 O 1118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2322 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 16, 'TRANS': 285} Chain: "B" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 371 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 7, 'TRANS': 39} Chain: "H" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 14, 'TRANS': 205} Chain: "L" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1657 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Time building chain proxies: 3.87, per 1000 atoms: 0.64 Number of scatterers: 6016 At special positions: 0 Unit cell: (70.965, 73.455, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1118 8.00 N 976 7.00 C 3880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 958.2 milliseconds 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1446 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 11 sheets defined 35.8% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 58 through 84 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.643A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 3.699A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.548A pdb=" N VAL A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 4.949A pdb=" N LYS A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.065A pdb=" N ALA A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix removed outlier: 3.562A pdb=" N PHE A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.609A pdb=" N GLY A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 4.252A pdb=" N CYS A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 312 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.873A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.716A pdb=" N THR L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 189 removed outlier: 4.155A pdb=" N HIS L 189 " --> pdb=" O TYR L 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.590A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.683A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.532A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.532A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 158 through 160 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.501A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.434A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.780A pdb=" N ASN L 137 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 149 removed outlier: 5.680A pdb=" N HIS L 198 " --> pdb=" O SER L 203 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER L 203 " --> pdb=" O HIS L 198 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1856 1.34 - 1.46: 1385 1.46 - 1.58: 2863 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 6168 Sorted by residual: bond pdb=" CB ASP H 73 " pdb=" CG ASP H 73 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.41e+00 bond pdb=" CG ARG A 143 " pdb=" CD ARG A 143 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CA TYR A 146 " pdb=" C TYR A 146 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.11e+00 bond pdb=" CB PRO A 181 " pdb=" CG PRO A 181 " ideal model delta sigma weight residual 1.492 1.543 -0.051 5.00e-02 4.00e+02 1.04e+00 bond pdb=" C VAL A 187 " pdb=" O VAL A 187 " ideal model delta sigma weight residual 1.233 1.243 -0.010 1.02e-02 9.61e+03 9.41e-01 ... (remaining 6163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 8279 2.42 - 4.84: 90 4.84 - 7.27: 20 7.27 - 9.69: 2 9.69 - 12.11: 1 Bond angle restraints: 8392 Sorted by residual: angle pdb=" C ASN H 140 " pdb=" CA ASN H 140 " pdb=" CB ASN H 140 " ideal model delta sigma weight residual 116.54 110.42 6.12 1.15e+00 7.56e-01 2.83e+01 angle pdb=" N ILE L 75 " pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 113.42 108.86 4.56 1.17e+00 7.31e-01 1.52e+01 angle pdb=" CA ASN H 140 " pdb=" C ASN H 140 " pdb=" N SER H 141 " ideal model delta sigma weight residual 119.52 116.78 2.74 7.90e-01 1.60e+00 1.20e+01 angle pdb=" CA LEU A 197 " pdb=" CB LEU A 197 " pdb=" CG LEU A 197 " ideal model delta sigma weight residual 116.30 128.41 -12.11 3.50e+00 8.16e-02 1.20e+01 angle pdb=" CG ARG A 143 " pdb=" CD ARG A 143 " pdb=" NE ARG A 143 " ideal model delta sigma weight residual 112.00 118.15 -6.15 2.20e+00 2.07e-01 7.82e+00 ... (remaining 8387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 3098 16.20 - 32.40: 432 32.40 - 48.59: 113 48.59 - 64.79: 17 64.79 - 80.99: 5 Dihedral angle restraints: 3665 sinusoidal: 1408 harmonic: 2257 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.21 41.79 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 60.92 32.08 1 1.00e+01 1.00e-02 1.47e+01 dihedral pdb=" CA PRO A 181 " pdb=" C PRO A 181 " pdb=" N GLN A 182 " pdb=" CA GLN A 182 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 3662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 660 0.037 - 0.075: 209 0.075 - 0.112: 83 0.112 - 0.149: 7 0.149 - 0.187: 2 Chirality restraints: 961 Sorted by residual: chirality pdb=" CB ILE A 291 " pdb=" CA ILE A 291 " pdb=" CG1 ILE A 291 " pdb=" CG2 ILE A 291 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ASP H 90 " pdb=" N ASP H 90 " pdb=" C ASP H 90 " pdb=" CB ASP H 90 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 958 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 180 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO A 181 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 82 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" CG ASP L 82 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP L 82 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP L 82 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 185 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" CD GLU L 185 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU L 185 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU L 185 " -0.012 2.00e-02 2.50e+03 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1042 2.76 - 3.30: 5747 3.30 - 3.83: 9895 3.83 - 4.37: 11414 4.37 - 4.90: 20185 Nonbonded interactions: 48283 Sorted by model distance: nonbonded pdb=" OG1 THR H 28 " pdb=" OD1 ASN H 31 " model vdw 2.228 3.040 nonbonded pdb=" O SER H 179 " pdb=" OG SER H 179 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS L 149 " pdb=" OE2 GLU L 195 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASN A 106 " pdb=" OG SER A 119 " model vdw 2.270 3.040 nonbonded pdb=" N GLU L 154 " pdb=" OE1 GLU L 154 " model vdw 2.276 3.120 ... (remaining 48278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6171 Z= 0.143 Angle : 0.662 12.108 8398 Z= 0.339 Chirality : 0.042 0.187 961 Planarity : 0.006 0.124 1050 Dihedral : 15.757 80.986 2210 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.74 % Allowed : 28.74 % Favored : 70.52 % 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: 0.28 (0.31), residues: 774 helix: 1.85 (0.33), residues: 240 sheet: 0.63 (0.36), residues: 218 loop : -1.51 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 189 PHE 0.006 0.001 PHE A 283 TYR 0.014 0.001 TYR A 307 ARG 0.015 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.17019 ( 291) hydrogen bonds : angle 7.27169 ( 864) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.85525 ( 6) covalent geometry : bond 0.00323 ( 6168) covalent geometry : angle 0.66146 ( 8392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 172 time to evaluate : 0.633 Fit side-chains REVERT: A 180 ARG cc_start: 0.7410 (ptp-170) cc_final: 0.7098 (ptp-110) REVERT: A 183 TYR cc_start: 0.7114 (m-80) cc_final: 0.6799 (m-80) outliers start: 5 outliers final: 4 residues processed: 172 average time/residue: 0.1574 time to fit residues: 36.2339 Evaluate side-chains 172 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.090264 restraints weight = 9657.440| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.76 r_work: 0.2837 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6171 Z= 0.164 Angle : 0.632 11.571 8398 Z= 0.313 Chirality : 0.044 0.150 961 Planarity : 0.005 0.079 1050 Dihedral : 4.876 39.031 837 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.15 % Allowed : 24.89 % Favored : 70.96 % 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: 0.33 (0.30), residues: 774 helix: 1.92 (0.33), residues: 242 sheet: 0.64 (0.36), residues: 217 loop : -1.52 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 106 HIS 0.003 0.001 HIS L 91 PHE 0.009 0.001 PHE H 153 TYR 0.015 0.001 TYR L 49 ARG 0.006 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 291) hydrogen bonds : angle 5.04329 ( 864) SS BOND : bond 0.00644 ( 3) SS BOND : angle 1.10989 ( 6) covalent geometry : bond 0.00385 ( 6168) covalent geometry : angle 0.63198 ( 8392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.735 Fit side-chains REVERT: A 180 ARG cc_start: 0.7365 (ptp-170) cc_final: 0.6951 (ptp-110) REVERT: A 183 TYR cc_start: 0.7118 (m-80) cc_final: 0.6765 (m-80) REVERT: H 73 ASP cc_start: 0.8451 (t0) cc_final: 0.8241 (t0) outliers start: 28 outliers final: 17 residues processed: 188 average time/residue: 0.1609 time to fit residues: 40.4686 Evaluate side-chains 181 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.086735 restraints weight = 9951.433| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.76 r_work: 0.2782 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 6171 Z= 0.259 Angle : 0.682 12.143 8398 Z= 0.340 Chirality : 0.046 0.154 961 Planarity : 0.005 0.066 1050 Dihedral : 4.626 20.014 829 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.72 % Favored : 93.15 % Rotamer: Outliers : 7.56 % Allowed : 22.67 % Favored : 69.78 % 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: 0.19 (0.31), residues: 774 helix: 1.83 (0.33), residues: 242 sheet: 0.56 (0.37), residues: 216 loop : -1.61 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.005 0.001 HIS L 91 PHE 0.015 0.002 PHE H 153 TYR 0.015 0.002 TYR L 30 ARG 0.008 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 291) hydrogen bonds : angle 4.72487 ( 864) SS BOND : bond 0.00296 ( 3) SS BOND : angle 1.65025 ( 6) covalent geometry : bond 0.00620 ( 6168) covalent geometry : angle 0.68048 ( 8392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9182 (mt) cc_final: 0.8921 (mt) REVERT: A 180 ARG cc_start: 0.7389 (ptp-170) cc_final: 0.6868 (ptp-110) REVERT: A 183 TYR cc_start: 0.7166 (m-80) cc_final: 0.6716 (m-80) REVERT: A 254 VAL cc_start: 0.8903 (t) cc_final: 0.8646 (p) REVERT: H 73 ASP cc_start: 0.8587 (t0) cc_final: 0.8265 (t0) REVERT: L 78 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8439 (tp) REVERT: L 134 CYS cc_start: 0.8674 (t) cc_final: 0.8417 (t) REVERT: L 193 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8457 (t) outliers start: 51 outliers final: 37 residues processed: 203 average time/residue: 0.1573 time to fit residues: 42.4029 Evaluate side-chains 206 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 61 optimal weight: 0.0370 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.091385 restraints weight = 9804.436| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.79 r_work: 0.2854 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6171 Z= 0.124 Angle : 0.608 12.157 8398 Z= 0.296 Chirality : 0.043 0.151 961 Planarity : 0.005 0.061 1050 Dihedral : 4.292 19.595 829 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 6.07 % Allowed : 25.33 % Favored : 68.59 % 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: 0.29 (0.31), residues: 774 helix: 1.99 (0.33), residues: 249 sheet: 0.61 (0.37), residues: 214 loop : -1.68 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 35 HIS 0.002 0.001 HIS L 198 PHE 0.008 0.001 PHE B 23 TYR 0.014 0.001 TYR L 49 ARG 0.009 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 291) hydrogen bonds : angle 4.41011 ( 864) SS BOND : bond 0.00516 ( 3) SS BOND : angle 1.16060 ( 6) covalent geometry : bond 0.00287 ( 6168) covalent geometry : angle 0.60742 ( 8392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9156 (mt) cc_final: 0.8893 (mt) REVERT: A 180 ARG cc_start: 0.7425 (ptp-170) cc_final: 0.6704 (ptp-170) REVERT: A 183 TYR cc_start: 0.7429 (m-80) cc_final: 0.6874 (m-80) REVERT: A 254 VAL cc_start: 0.8880 (t) cc_final: 0.8637 (p) REVERT: H 73 ASP cc_start: 0.8382 (t0) cc_final: 0.7959 (t0) REVERT: L 82 ASP cc_start: 0.9095 (p0) cc_final: 0.8811 (p0) REVERT: L 132 VAL cc_start: 0.8994 (t) cc_final: 0.8773 (t) REVERT: L 134 CYS cc_start: 0.8117 (t) cc_final: 0.7828 (t) REVERT: L 149 LYS cc_start: 0.9067 (mttp) cc_final: 0.8864 (mttp) REVERT: L 193 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8372 (t) outliers start: 41 outliers final: 25 residues processed: 211 average time/residue: 0.1744 time to fit residues: 48.1618 Evaluate side-chains 196 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 203 ASN L 76 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.089197 restraints weight = 9871.376| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.84 r_work: 0.2813 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6171 Z= 0.192 Angle : 0.639 12.670 8398 Z= 0.314 Chirality : 0.045 0.181 961 Planarity : 0.005 0.056 1050 Dihedral : 4.416 21.361 829 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 6.81 % Allowed : 25.33 % Favored : 67.85 % 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: 0.24 (0.31), residues: 774 helix: 1.92 (0.33), residues: 249 sheet: 0.60 (0.37), residues: 214 loop : -1.70 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 91 PHE 0.010 0.001 PHE A 37 TYR 0.015 0.001 TYR L 192 ARG 0.010 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 291) hydrogen bonds : angle 4.41214 ( 864) SS BOND : bond 0.00473 ( 3) SS BOND : angle 1.24113 ( 6) covalent geometry : bond 0.00463 ( 6168) covalent geometry : angle 0.63857 ( 8392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9222 (mt) cc_final: 0.8926 (mt) REVERT: A 180 ARG cc_start: 0.7583 (ptp-170) cc_final: 0.6618 (ptp-170) REVERT: A 183 TYR cc_start: 0.7481 (m-80) cc_final: 0.6840 (m-80) REVERT: A 254 VAL cc_start: 0.8894 (t) cc_final: 0.8607 (p) REVERT: H 73 ASP cc_start: 0.8520 (t0) cc_final: 0.8068 (t0) REVERT: L 134 CYS cc_start: 0.8680 (t) cc_final: 0.8382 (t) REVERT: L 193 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8379 (t) outliers start: 46 outliers final: 36 residues processed: 198 average time/residue: 0.1665 time to fit residues: 43.7625 Evaluate side-chains 195 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 203 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.089931 restraints weight = 9702.017| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.75 r_work: 0.2849 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6171 Z= 0.138 Angle : 0.628 13.278 8398 Z= 0.303 Chirality : 0.044 0.164 961 Planarity : 0.005 0.055 1050 Dihedral : 4.296 20.855 829 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.22 % Allowed : 27.11 % Favored : 66.67 % 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: 0.21 (0.31), residues: 774 helix: 1.86 (0.33), residues: 254 sheet: 0.61 (0.37), residues: 214 loop : -1.77 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 91 PHE 0.008 0.001 PHE B 23 TYR 0.015 0.001 TYR L 192 ARG 0.010 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 291) hydrogen bonds : angle 4.31360 ( 864) SS BOND : bond 0.00443 ( 3) SS BOND : angle 0.95356 ( 6) covalent geometry : bond 0.00324 ( 6168) covalent geometry : angle 0.62782 ( 8392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9246 (mt) cc_final: 0.8988 (mt) REVERT: A 180 ARG cc_start: 0.7520 (ptp-170) cc_final: 0.6596 (ptp-170) REVERT: A 183 TYR cc_start: 0.7471 (m-80) cc_final: 0.6845 (m-80) REVERT: A 254 VAL cc_start: 0.8947 (t) cc_final: 0.8608 (p) REVERT: H 73 ASP cc_start: 0.8446 (t0) cc_final: 0.7995 (t0) REVERT: L 132 VAL cc_start: 0.9187 (t) cc_final: 0.8985 (t) REVERT: L 134 CYS cc_start: 0.8592 (t) cc_final: 0.8310 (t) REVERT: L 193 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8460 (t) outliers start: 42 outliers final: 35 residues processed: 205 average time/residue: 0.1588 time to fit residues: 43.6877 Evaluate side-chains 204 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.090964 restraints weight = 9708.957| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.84 r_work: 0.2859 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6171 Z= 0.127 Angle : 0.623 13.462 8398 Z= 0.299 Chirality : 0.043 0.152 961 Planarity : 0.005 0.052 1050 Dihedral : 4.198 19.414 829 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.81 % Allowed : 26.52 % Favored : 66.67 % 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: 0.23 (0.31), residues: 774 helix: 1.85 (0.33), residues: 255 sheet: 0.64 (0.37), residues: 214 loop : -1.75 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS L 91 PHE 0.008 0.001 PHE A 310 TYR 0.019 0.001 TYR L 192 ARG 0.012 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 291) hydrogen bonds : angle 4.23346 ( 864) SS BOND : bond 0.00483 ( 3) SS BOND : angle 1.00187 ( 6) covalent geometry : bond 0.00297 ( 6168) covalent geometry : angle 0.62242 ( 8392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9206 (mt) cc_final: 0.8953 (mt) REVERT: A 180 ARG cc_start: 0.7514 (ptp-170) cc_final: 0.6513 (ptp-170) REVERT: A 183 TYR cc_start: 0.7448 (m-80) cc_final: 0.6816 (m-80) REVERT: H 73 ASP cc_start: 0.8416 (t0) cc_final: 0.7868 (t0) REVERT: H 112 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8549 (pt0) REVERT: L 132 VAL cc_start: 0.8994 (t) cc_final: 0.8790 (t) REVERT: L 134 CYS cc_start: 0.8228 (t) cc_final: 0.7901 (t) REVERT: L 193 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8394 (t) REVERT: L 207 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7920 (mptt) outliers start: 46 outliers final: 32 residues processed: 212 average time/residue: 0.1580 time to fit residues: 44.8248 Evaluate side-chains 206 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.091089 restraints weight = 9719.655| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.84 r_work: 0.2867 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6171 Z= 0.128 Angle : 0.632 14.310 8398 Z= 0.301 Chirality : 0.043 0.203 961 Planarity : 0.005 0.056 1050 Dihedral : 4.161 19.453 829 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.78 % Allowed : 28.00 % Favored : 66.22 % 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: 0.21 (0.30), residues: 774 helix: 1.82 (0.33), residues: 248 sheet: 0.63 (0.37), residues: 214 loop : -1.67 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.000 HIS L 91 PHE 0.008 0.001 PHE A 310 TYR 0.012 0.001 TYR L 49 ARG 0.014 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 291) hydrogen bonds : angle 4.21595 ( 864) SS BOND : bond 0.00482 ( 3) SS BOND : angle 0.96710 ( 6) covalent geometry : bond 0.00301 ( 6168) covalent geometry : angle 0.63157 ( 8392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9203 (mt) cc_final: 0.8958 (mt) REVERT: A 180 ARG cc_start: 0.7626 (ptp-170) cc_final: 0.6561 (ptp-170) REVERT: A 183 TYR cc_start: 0.7299 (m-80) cc_final: 0.6709 (m-80) REVERT: A 254 VAL cc_start: 0.8928 (t) cc_final: 0.8673 (p) REVERT: H 73 ASP cc_start: 0.8376 (t0) cc_final: 0.7829 (t0) REVERT: H 112 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8510 (pt0) REVERT: L 132 VAL cc_start: 0.8991 (t) cc_final: 0.8789 (t) REVERT: L 134 CYS cc_start: 0.8215 (t) cc_final: 0.7893 (t) REVERT: L 193 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8412 (t) REVERT: L 207 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7904 (mptt) outliers start: 39 outliers final: 35 residues processed: 205 average time/residue: 0.1715 time to fit residues: 47.5498 Evaluate side-chains 210 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.091608 restraints weight = 9671.579| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.83 r_work: 0.2867 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6171 Z= 0.130 Angle : 0.641 14.502 8398 Z= 0.304 Chirality : 0.043 0.198 961 Planarity : 0.005 0.060 1050 Dihedral : 4.129 19.072 829 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.22 % Allowed : 27.41 % Favored : 66.37 % 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: 0.21 (0.30), residues: 774 helix: 1.79 (0.33), residues: 248 sheet: 0.70 (0.37), residues: 214 loop : -1.69 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.000 HIS L 91 PHE 0.008 0.001 PHE B 23 TYR 0.012 0.001 TYR L 49 ARG 0.014 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 291) hydrogen bonds : angle 4.19934 ( 864) SS BOND : bond 0.00487 ( 3) SS BOND : angle 1.01906 ( 6) covalent geometry : bond 0.00306 ( 6168) covalent geometry : angle 0.64028 ( 8392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9241 (mt) cc_final: 0.8989 (mt) REVERT: A 180 ARG cc_start: 0.7601 (ptp-170) cc_final: 0.6585 (ptp-170) REVERT: A 183 TYR cc_start: 0.7351 (m-80) cc_final: 0.6734 (m-80) REVERT: A 254 VAL cc_start: 0.8988 (t) cc_final: 0.8705 (p) REVERT: H 13 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8205 (mmm160) REVERT: H 73 ASP cc_start: 0.8476 (t0) cc_final: 0.7822 (t0) REVERT: H 112 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: L 132 VAL cc_start: 0.9142 (t) cc_final: 0.8939 (t) REVERT: L 134 CYS cc_start: 0.8586 (t) cc_final: 0.8306 (t) REVERT: L 193 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8504 (t) REVERT: L 207 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7964 (mptt) outliers start: 42 outliers final: 33 residues processed: 204 average time/residue: 0.1471 time to fit residues: 40.3811 Evaluate side-chains 207 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.0470 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 0.0070 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.093603 restraints weight = 9754.807| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.79 r_work: 0.2899 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6171 Z= 0.115 Angle : 0.636 14.827 8398 Z= 0.301 Chirality : 0.043 0.204 961 Planarity : 0.005 0.063 1050 Dihedral : 4.052 18.555 829 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.89 % Allowed : 28.89 % Favored : 66.22 % 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: 0.26 (0.30), residues: 774 helix: 1.80 (0.33), residues: 248 sheet: 0.73 (0.36), residues: 216 loop : -1.66 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.002 0.000 HIS L 91 PHE 0.007 0.001 PHE A 310 TYR 0.013 0.001 TYR L 192 ARG 0.015 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 291) hydrogen bonds : angle 4.13293 ( 864) SS BOND : bond 0.00553 ( 3) SS BOND : angle 0.88771 ( 6) covalent geometry : bond 0.00263 ( 6168) covalent geometry : angle 0.63558 ( 8392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9266 (mt) cc_final: 0.9013 (mt) REVERT: A 180 ARG cc_start: 0.7590 (ptp-170) cc_final: 0.6592 (ptp-110) REVERT: A 183 TYR cc_start: 0.7327 (m-80) cc_final: 0.6755 (m-80) REVERT: A 254 VAL cc_start: 0.8931 (t) cc_final: 0.8679 (p) REVERT: H 13 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8193 (mmm160) REVERT: H 73 ASP cc_start: 0.8365 (t0) cc_final: 0.7683 (t0) REVERT: H 112 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: L 4 MET cc_start: 0.8800 (tpp) cc_final: 0.8366 (mmm) REVERT: L 32 TYR cc_start: 0.9221 (m-10) cc_final: 0.8913 (m-10) REVERT: L 132 VAL cc_start: 0.8984 (t) cc_final: 0.8783 (t) REVERT: L 134 CYS cc_start: 0.8229 (t) cc_final: 0.7930 (t) REVERT: L 193 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8443 (t) REVERT: L 207 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7763 (mptt) outliers start: 33 outliers final: 30 residues processed: 204 average time/residue: 0.1428 time to fit residues: 39.3964 Evaluate side-chains 208 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 63 optimal weight: 0.0570 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.093606 restraints weight = 9849.025| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.86 r_work: 0.2910 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6171 Z= 0.115 Angle : 0.637 14.734 8398 Z= 0.302 Chirality : 0.043 0.201 961 Planarity : 0.005 0.062 1050 Dihedral : 3.985 18.545 829 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.30 % Allowed : 29.48 % Favored : 66.22 % 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: 0.31 (0.31), residues: 774 helix: 1.81 (0.33), residues: 255 sheet: 0.77 (0.37), residues: 216 loop : -1.71 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 106 HIS 0.001 0.000 HIS L 91 PHE 0.007 0.001 PHE A 310 TYR 0.017 0.001 TYR A 69 ARG 0.015 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 291) hydrogen bonds : angle 4.06948 ( 864) SS BOND : bond 0.00492 ( 3) SS BOND : angle 0.91981 ( 6) covalent geometry : bond 0.00263 ( 6168) covalent geometry : angle 0.63669 ( 8392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.97 seconds wall clock time: 57 minutes 42.55 seconds (3462.55 seconds total)