Starting phenix.real_space_refine on Fri Aug 22 16:42:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hry_34982/08_2025/8hry_34982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hry_34982/08_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_34982/08_2025/8hry_34982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hry_34982/08_2025/8hry_34982.map" model { file = "/net/cci-nas-00/data/ceres_data/8hry_34982/08_2025/8hry_34982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hry_34982/08_2025/8hry_34982.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.35, per 1000 atoms: 0.22 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: 0.39 Conformation dependent library (CDL) restraints added in 197.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.23 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: 0.94 Time building geometry restraints manager: 0.55 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.080 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.110 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (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 ARG 0.015 0.001 ARG A 143 TYR 0.014 0.001 TYR A 307 PHE 0.006 0.001 PHE A 283 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6168) covalent geometry : angle 0.66146 ( 8392) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.85525 ( 6) hydrogen bonds : bond 0.17019 ( 291) hydrogen bonds : angle 7.27169 ( 864) *********************** 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 : 0.237 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: 0.0708 time to fit residues: 16.4345 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 : 0.268 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.110105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.090196 restraints weight = 9740.563| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.77 r_work: 0.2838 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6171 Z= 0.164 Angle : 0.631 11.228 8398 Z= 0.312 Chirality : 0.044 0.150 961 Planarity : 0.005 0.080 1050 Dihedral : 4.889 38.797 837 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.89 % Allowed : 24.00 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.31), residues: 774 helix: 1.94 (0.33), residues: 242 sheet: 0.63 (0.36), residues: 217 loop : -1.51 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 143 TYR 0.017 0.001 TYR L 49 PHE 0.010 0.001 PHE H 153 TRP 0.009 0.001 TRP H 106 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6168) covalent geometry : angle 0.63018 ( 8392) SS BOND : bond 0.00690 ( 3) SS BOND : angle 1.19233 ( 6) hydrogen bonds : bond 0.04118 ( 291) hydrogen bonds : angle 4.83962 ( 864) *********************** 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 208 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.216 Fit side-chains REVERT: A 180 ARG cc_start: 0.7344 (ptp-170) cc_final: 0.6911 (ptp-110) REVERT: A 183 TYR cc_start: 0.7111 (m-80) cc_final: 0.6752 (m-80) REVERT: H 73 ASP cc_start: 0.8449 (t0) cc_final: 0.8147 (t0) outliers start: 33 outliers final: 24 residues processed: 195 average time/residue: 0.0642 time to fit residues: 16.9346 Evaluate side-chains 189 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 176 LEU 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 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 62 GLU Chi-restraints excluded: chain H residue 91 SER 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 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.108609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.088816 restraints weight = 9878.794| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.76 r_work: 0.2807 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 6171 Z= 0.196 Angle : 0.643 12.690 8398 Z= 0.317 Chirality : 0.045 0.154 961 Planarity : 0.005 0.066 1050 Dihedral : 4.537 26.192 831 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.94 % Favored : 93.93 % Rotamer: Outliers : 7.11 % Allowed : 22.52 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.31), residues: 774 helix: 1.91 (0.33), residues: 242 sheet: 0.59 (0.37), residues: 216 loop : -1.57 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 143 TYR 0.013 0.001 TYR A 69 PHE 0.011 0.001 PHE H 153 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 6168) covalent geometry : angle 0.64188 ( 8392) SS BOND : bond 0.00371 ( 3) SS BOND : angle 1.55922 ( 6) hydrogen bonds : bond 0.04135 ( 291) hydrogen bonds : angle 4.59131 ( 864) *********************** 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 215 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.218 Fit side-chains REVERT: A 165 LEU cc_start: 0.9205 (mt) cc_final: 0.8959 (mt) REVERT: A 180 ARG cc_start: 0.7393 (ptp-170) cc_final: 0.6876 (ptp-110) REVERT: A 183 TYR cc_start: 0.7139 (m-80) cc_final: 0.6716 (m-80) REVERT: A 254 VAL cc_start: 0.8886 (t) cc_final: 0.8641 (p) REVERT: H 73 ASP cc_start: 0.8490 (t0) cc_final: 0.8111 (t0) REVERT: L 134 CYS cc_start: 0.8564 (t) cc_final: 0.8337 (t) outliers start: 48 outliers final: 37 residues processed: 199 average time/residue: 0.0708 time to fit residues: 18.8309 Evaluate side-chains 199 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 117 ASN 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 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 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 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 176 SER Chi-restraints excluded: chain L residue 182 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 62 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.109371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.089984 restraints weight = 9755.428| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.73 r_work: 0.2845 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6171 Z= 0.138 Angle : 0.605 12.258 8398 Z= 0.296 Chirality : 0.043 0.150 961 Planarity : 0.004 0.060 1050 Dihedral : 4.281 20.050 829 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 7.26 % Allowed : 23.26 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.31), residues: 774 helix: 1.80 (0.33), residues: 255 sheet: 0.67 (0.37), residues: 214 loop : -1.70 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 143 TYR 0.014 0.001 TYR L 49 PHE 0.007 0.001 PHE H 153 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6168) covalent geometry : angle 0.60400 ( 8392) SS BOND : bond 0.00467 ( 3) SS BOND : angle 1.22084 ( 6) hydrogen bonds : bond 0.03752 ( 291) hydrogen bonds : angle 4.39385 ( 864) *********************** 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 226 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 0.220 Fit side-chains REVERT: A 165 LEU cc_start: 0.9213 (mt) cc_final: 0.8941 (mt) REVERT: A 180 ARG cc_start: 0.7446 (ptp-170) cc_final: 0.6724 (ptp-170) REVERT: A 183 TYR cc_start: 0.7458 (m-80) cc_final: 0.6883 (m-80) REVERT: A 254 VAL cc_start: 0.8933 (t) cc_final: 0.8672 (p) REVERT: H 73 ASP cc_start: 0.8467 (t0) cc_final: 0.8040 (t0) REVERT: L 76 ASN cc_start: 0.8918 (m-40) cc_final: 0.8713 (m110) REVERT: L 132 VAL cc_start: 0.9122 (t) cc_final: 0.8890 (t) REVERT: L 134 CYS cc_start: 0.8532 (t) cc_final: 0.8292 (t) REVERT: L 149 LYS cc_start: 0.9129 (mttp) cc_final: 0.8919 (mttp) REVERT: L 193 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8463 (t) outliers start: 49 outliers final: 33 residues processed: 212 average time/residue: 0.0688 time to fit residues: 19.5888 Evaluate side-chains 205 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 210 VAL Chi-restraints excluded: chain A residue 218 MET 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 57 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** 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 = 0.3302 r_free = 0.3302 target = 0.111463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.090959 restraints weight = 9873.436| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.85 r_work: 0.2859 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6171 Z= 0.127 Angle : 0.613 13.042 8398 Z= 0.297 Chirality : 0.043 0.182 961 Planarity : 0.005 0.057 1050 Dihedral : 4.198 20.825 829 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 6.81 % Allowed : 25.19 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.31), residues: 774 helix: 1.82 (0.33), residues: 255 sheet: 0.69 (0.37), residues: 214 loop : -1.73 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 143 TYR 0.019 0.001 TYR L 192 PHE 0.007 0.001 PHE A 310 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.000 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6168) covalent geometry : angle 0.61275 ( 8392) SS BOND : bond 0.00502 ( 3) SS BOND : angle 1.08395 ( 6) hydrogen bonds : bond 0.03600 ( 291) hydrogen bonds : angle 4.28189 ( 864) *********************** 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 224 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9202 (mt) cc_final: 0.8962 (mt) REVERT: A 180 ARG cc_start: 0.7476 (ptp-170) cc_final: 0.6552 (ptp-170) REVERT: A 183 TYR cc_start: 0.7494 (m-80) cc_final: 0.6914 (m-80) REVERT: A 254 VAL cc_start: 0.8835 (t) cc_final: 0.8535 (p) REVERT: H 73 ASP cc_start: 0.8387 (t0) cc_final: 0.7948 (t0) REVERT: H 112 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8874 (pm20) REVERT: L 76 ASN cc_start: 0.8901 (m-40) cc_final: 0.8686 (m110) REVERT: L 134 CYS cc_start: 0.8156 (t) cc_final: 0.7848 (t) REVERT: L 193 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8398 (t) REVERT: L 207 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7964 (mptt) outliers start: 46 outliers final: 33 residues processed: 214 average time/residue: 0.0657 time to fit residues: 19.1366 Evaluate side-chains 211 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 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 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 104 LEU 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 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 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.108202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.088112 restraints weight = 9839.882| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.81 r_work: 0.2834 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6171 Z= 0.184 Angle : 0.642 13.011 8398 Z= 0.313 Chirality : 0.044 0.155 961 Planarity : 0.005 0.054 1050 Dihedral : 4.365 20.926 829 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.31), residues: 774 helix: 1.74 (0.33), residues: 255 sheet: 0.69 (0.37), residues: 214 loop : -1.76 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 143 TYR 0.012 0.001 TYR L 49 PHE 0.009 0.001 PHE H 153 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 6168) covalent geometry : angle 0.64154 ( 8392) SS BOND : bond 0.00453 ( 3) SS BOND : angle 1.18381 ( 6) hydrogen bonds : bond 0.03867 ( 291) hydrogen bonds : angle 4.34154 ( 864) *********************** 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 220 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9145 (mt) cc_final: 0.8845 (mt) REVERT: A 180 ARG cc_start: 0.7583 (ptp-170) cc_final: 0.6536 (ptp-170) REVERT: A 183 TYR cc_start: 0.7453 (m-80) cc_final: 0.6800 (m-80) REVERT: A 254 VAL cc_start: 0.8840 (t) cc_final: 0.8532 (p) REVERT: H 73 ASP cc_start: 0.8391 (t0) cc_final: 0.7917 (t0) REVERT: L 134 CYS cc_start: 0.8242 (t) cc_final: 0.7906 (t) REVERT: L 193 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8362 (t) REVERT: L 207 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7925 (mptt) outliers start: 46 outliers final: 38 residues processed: 207 average time/residue: 0.0618 time to fit residues: 17.3390 Evaluate side-chains 204 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 131 LEU 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 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 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 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 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 207 LYS 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 1 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 35 optimal weight: 0.0060 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.113325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.093369 restraints weight = 9738.967| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.85 r_work: 0.2881 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6171 Z= 0.117 Angle : 0.624 13.582 8398 Z= 0.298 Chirality : 0.043 0.150 961 Planarity : 0.005 0.053 1050 Dihedral : 4.161 19.658 829 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.59 % Allowed : 28.30 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.31), residues: 774 helix: 1.82 (0.32), residues: 255 sheet: 0.72 (0.37), residues: 216 loop : -1.75 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 143 TYR 0.013 0.001 TYR L 49 PHE 0.008 0.001 PHE A 310 TRP 0.009 0.001 TRP L 35 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6168) covalent geometry : angle 0.62395 ( 8392) SS BOND : bond 0.00506 ( 3) SS BOND : angle 0.97208 ( 6) hydrogen bonds : bond 0.03522 ( 291) hydrogen bonds : angle 4.24205 ( 864) *********************** 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 221 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9194 (mt) cc_final: 0.8949 (mt) REVERT: A 180 ARG cc_start: 0.7511 (ptp-170) cc_final: 0.6525 (ptp-170) REVERT: A 183 TYR cc_start: 0.7429 (m-80) cc_final: 0.6864 (m-80) REVERT: A 254 VAL cc_start: 0.8927 (t) cc_final: 0.8643 (p) REVERT: H 59 ASN cc_start: 0.9164 (t0) cc_final: 0.8951 (t0) REVERT: H 73 ASP cc_start: 0.8303 (t0) cc_final: 0.7838 (t0) REVERT: H 112 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8814 (pm20) REVERT: L 4 MET cc_start: 0.8826 (tpp) cc_final: 0.8425 (mmm) REVERT: L 32 TYR cc_start: 0.9213 (m-10) cc_final: 0.8934 (m-10) REVERT: L 76 ASN cc_start: 0.8890 (m-40) cc_final: 0.8686 (m110) REVERT: L 134 CYS cc_start: 0.8111 (t) cc_final: 0.7785 (t) REVERT: L 186 TYR cc_start: 0.9328 (t80) cc_final: 0.9124 (t80) REVERT: L 193 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8315 (t) REVERT: L 207 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7862 (mptt) outliers start: 31 outliers final: 21 residues processed: 213 average time/residue: 0.0604 time to fit residues: 17.5375 Evaluate side-chains 203 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 236 LEU 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 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 58 VAL Chi-restraints excluded: chain L residue 105 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.110440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.089989 restraints weight = 9833.565| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.82 r_work: 0.2841 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6171 Z= 0.165 Angle : 0.650 13.986 8398 Z= 0.313 Chirality : 0.044 0.198 961 Planarity : 0.005 0.052 1050 Dihedral : 4.261 20.034 829 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.78 % Allowed : 26.96 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.31), residues: 774 helix: 1.74 (0.32), residues: 256 sheet: 0.72 (0.37), residues: 216 loop : -1.74 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 143 TYR 0.014 0.001 TYR L 192 PHE 0.007 0.001 PHE A 234 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 6168) covalent geometry : angle 0.65005 ( 8392) SS BOND : bond 0.00468 ( 3) SS BOND : angle 1.11116 ( 6) hydrogen bonds : bond 0.03723 ( 291) hydrogen bonds : angle 4.26215 ( 864) *********************** 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 213 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9193 (mt) cc_final: 0.8928 (mt) REVERT: A 180 ARG cc_start: 0.7604 (ptp-170) cc_final: 0.6606 (ptp-170) REVERT: A 183 TYR cc_start: 0.7361 (m-80) cc_final: 0.6756 (m-80) REVERT: A 229 MET cc_start: 0.8789 (ttm) cc_final: 0.8414 (ttt) REVERT: A 254 VAL cc_start: 0.8971 (t) cc_final: 0.8692 (p) REVERT: H 13 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8265 (mmm160) REVERT: H 73 ASP cc_start: 0.8321 (t0) cc_final: 0.7849 (t0) REVERT: L 76 ASN cc_start: 0.8881 (m-40) cc_final: 0.8656 (m110) REVERT: L 134 CYS cc_start: 0.8277 (t) cc_final: 0.7950 (t) REVERT: L 192 TYR cc_start: 0.9166 (m-80) cc_final: 0.8924 (m-80) REVERT: L 193 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8429 (t) REVERT: L 207 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7950 (mptt) outliers start: 39 outliers final: 33 residues processed: 203 average time/residue: 0.0605 time to fit residues: 16.5986 Evaluate side-chains 208 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 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 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 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 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 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 Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 57 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.110815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.091380 restraints weight = 9757.046| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.74 r_work: 0.2863 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6171 Z= 0.135 Angle : 0.644 13.835 8398 Z= 0.308 Chirality : 0.043 0.193 961 Planarity : 0.005 0.057 1050 Dihedral : 4.210 20.099 829 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.33 % Allowed : 27.70 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.31), residues: 774 helix: 1.74 (0.32), residues: 256 sheet: 0.76 (0.37), residues: 216 loop : -1.70 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 143 TYR 0.014 0.001 TYR L 192 PHE 0.007 0.001 PHE A 310 TRP 0.008 0.001 TRP H 106 HIS 0.002 0.000 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6168) covalent geometry : angle 0.64338 ( 8392) SS BOND : bond 0.00562 ( 3) SS BOND : angle 1.00591 ( 6) hydrogen bonds : bond 0.03603 ( 291) hydrogen bonds : angle 4.20891 ( 864) *********************** 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 209 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9233 (mt) cc_final: 0.8973 (mt) REVERT: A 180 ARG cc_start: 0.7602 (ptp-170) cc_final: 0.6606 (ptp-110) REVERT: A 183 TYR cc_start: 0.7387 (m-80) cc_final: 0.6758 (m-80) REVERT: A 229 MET cc_start: 0.8786 (ttm) cc_final: 0.8480 (ttt) REVERT: A 244 PHE cc_start: 0.8401 (m-80) cc_final: 0.8174 (m-80) REVERT: A 254 VAL cc_start: 0.9005 (t) cc_final: 0.8703 (p) REVERT: H 13 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8204 (mmm160) REVERT: H 73 ASP cc_start: 0.8417 (t0) cc_final: 0.7870 (t0) REVERT: L 76 ASN cc_start: 0.8925 (m-40) cc_final: 0.8707 (m110) REVERT: L 134 CYS cc_start: 0.8617 (t) cc_final: 0.8317 (t) REVERT: L 186 TYR cc_start: 0.9371 (t80) cc_final: 0.9136 (t80) REVERT: L 193 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8571 (t) REVERT: L 207 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7971 (mptt) outliers start: 36 outliers final: 27 residues processed: 200 average time/residue: 0.0596 time to fit residues: 16.1134 Evaluate side-chains 199 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 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 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 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 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.112510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.092326 restraints weight = 9731.798| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.83 r_work: 0.2872 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1617 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= 0.126 Angle : 0.644 14.546 8398 Z= 0.307 Chirality : 0.043 0.190 961 Planarity : 0.005 0.063 1050 Dihedral : 4.147 19.722 829 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.15 % Allowed : 29.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.31), residues: 774 helix: 1.79 (0.32), residues: 255 sheet: 0.79 (0.37), residues: 216 loop : -1.72 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 143 TYR 0.012 0.001 TYR L 49 PHE 0.007 0.001 PHE A 310 TRP 0.008 0.001 TRP H 106 HIS 0.002 0.000 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6168) covalent geometry : angle 0.64333 ( 8392) SS BOND : bond 0.00509 ( 3) SS BOND : angle 0.98191 ( 6) hydrogen bonds : bond 0.03510 ( 291) hydrogen bonds : angle 4.15798 ( 864) ********************** 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 209 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9176 (mt) cc_final: 0.8920 (mt) REVERT: A 180 ARG cc_start: 0.7591 (ptp-170) cc_final: 0.6601 (ptp-110) REVERT: A 183 TYR cc_start: 0.7374 (m-80) cc_final: 0.6787 (m-80) REVERT: A 254 VAL cc_start: 0.8907 (t) cc_final: 0.8641 (p) REVERT: H 13 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8181 (mmm160) REVERT: H 73 ASP cc_start: 0.8408 (t0) cc_final: 0.7779 (t0) REVERT: L 76 ASN cc_start: 0.8891 (m-40) cc_final: 0.8689 (m110) REVERT: L 134 CYS cc_start: 0.8239 (t) cc_final: 0.7910 (t) REVERT: L 193 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (t) REVERT: L 207 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7896 (mptt) outliers start: 28 outliers final: 25 residues processed: 204 average time/residue: 0.0566 time to fit residues: 15.6614 Evaluate side-chains 204 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 236 LEU 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 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 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 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 64 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 0.0020 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.111478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.091453 restraints weight = 9774.098| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.79 r_work: 0.2865 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6171 Z= 0.140 Angle : 0.655 14.514 8398 Z= 0.313 Chirality : 0.044 0.189 961 Planarity : 0.005 0.061 1050 Dihedral : 4.193 19.985 829 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.74 % Allowed : 28.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.31), residues: 774 helix: 1.77 (0.32), residues: 255 sheet: 0.80 (0.37), residues: 216 loop : -1.73 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 143 TYR 0.026 0.002 TYR L 186 PHE 0.007 0.001 PHE A 310 TRP 0.009 0.001 TRP H 195 HIS 0.002 0.000 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6168) covalent geometry : angle 0.65451 ( 8392) SS BOND : bond 0.00533 ( 3) SS BOND : angle 0.99569 ( 6) hydrogen bonds : bond 0.03588 ( 291) hydrogen bonds : angle 4.19078 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1531.00 seconds wall clock time: 26 minutes 55.95 seconds (1615.95 seconds total)