Starting phenix.real_space_refine on Thu Jun 5 11:04:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hry_34982/06_2025/8hry_34982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hry_34982/06_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_34982/06_2025/8hry_34982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hry_34982/06_2025/8hry_34982.map" model { file = "/net/cci-nas-00/data/ceres_data/8hry_34982/06_2025/8hry_34982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hry_34982/06_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 3.75, per 1000 atoms: 0.62 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: 1.30 Conformation dependent library (CDL) restraints added in 828.7 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: 0.65 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: 1.59 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: 0.480 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.820 Find NCS groups from input model: 0.060 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- 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 : 0.683 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: 0.1602 time to fit residues: 36.9031 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 : 0.635 ------------------------------------------------------------------------------- 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 = 0.110207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.090267 restraints weight = 9662.237| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.75 r_work: 0.2837 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 5.04322 ( 864) SS BOND : bond 0.00643 ( 3) SS BOND : angle 1.10989 ( 6) covalent geometry : bond 0.00385 ( 6168) covalent geometry : angle 0.63197 ( 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 : 0.662 Fit side-chains REVERT: A 180 ARG cc_start: 0.7367 (ptp-170) cc_final: 0.6955 (ptp-110) REVERT: A 183 TYR cc_start: 0.7116 (m-80) cc_final: 0.6765 (m-80) REVERT: H 73 ASP cc_start: 0.8454 (t0) cc_final: 0.8243 (t0) outliers start: 28 outliers final: 17 residues processed: 188 average time/residue: 0.1755 time to fit residues: 43.9638 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 : 0.719 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.107981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.088531 restraints weight = 9881.378| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.76 r_work: 0.2793 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 6171 Z= 0.230 Angle : 0.665 12.240 8398 Z= 0.331 Chirality : 0.046 0.153 961 Planarity : 0.005 0.067 1050 Dihedral : 4.569 19.955 829 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.72 % Favored : 93.15 % Rotamer: Outliers : 7.26 % Allowed : 22.81 % Favored : 69.93 % 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: 0.22 (0.31), residues: 774 helix: 1.86 (0.33), residues: 242 sheet: 0.56 (0.37), residues: 216 loop : -1.59 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS L 91 PHE 0.014 0.002 PHE H 153 TYR 0.014 0.002 TYR A 69 ARG 0.006 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 291) hydrogen bonds : angle 4.66913 ( 864) SS BOND : bond 0.00365 ( 3) SS BOND : angle 1.77164 ( 6) covalent geometry : bond 0.00551 ( 6168) covalent geometry : angle 0.66311 ( 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 219 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.763 Fit side-chains REVERT: A 165 LEU cc_start: 0.9191 (mt) cc_final: 0.8936 (mt) REVERT: A 180 ARG cc_start: 0.7384 (ptp-170) cc_final: 0.6863 (ptp-110) REVERT: A 183 TYR cc_start: 0.7151 (m-80) cc_final: 0.6718 (m-80) REVERT: A 254 VAL cc_start: 0.8892 (t) cc_final: 0.8642 (p) REVERT: H 73 ASP cc_start: 0.8567 (t0) cc_final: 0.8235 (t0) REVERT: L 193 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8455 (t) outliers start: 49 outliers final: 36 residues processed: 200 average time/residue: 0.1582 time to fit residues: 42.5399 Evaluate side-chains 202 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 20 optimal weight: 0.1980 chunk 61 optimal weight: 0.0470 chunk 30 optimal weight: 0.0050 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.3092 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.112552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.092873 restraints weight = 9725.147| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.77 r_work: 0.2885 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6171 Z= 0.111 Angle : 0.600 12.248 8398 Z= 0.291 Chirality : 0.043 0.151 961 Planarity : 0.004 0.061 1050 Dihedral : 4.180 19.574 829 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.78 % Allowed : 25.48 % Favored : 68.74 % 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 (0.31), residues: 774 helix: 1.84 (0.33), residues: 255 sheet: 0.67 (0.37), residues: 214 loop : -1.71 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 35 HIS 0.001 0.000 HIS L 198 PHE 0.008 0.001 PHE B 23 TYR 0.015 0.001 TYR L 49 ARG 0.007 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 291) hydrogen bonds : angle 4.35001 ( 864) SS BOND : bond 0.00356 ( 3) SS BOND : angle 1.31724 ( 6) covalent geometry : bond 0.00243 ( 6168) covalent geometry : angle 0.59878 ( 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 233 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.765 Fit side-chains REVERT: A 165 LEU cc_start: 0.9244 (mt) cc_final: 0.9020 (mt) REVERT: A 180 ARG cc_start: 0.7425 (ptp-170) cc_final: 0.6736 (ptp-170) REVERT: A 183 TYR cc_start: 0.7459 (m-80) cc_final: 0.6922 (m-80) REVERT: A 254 VAL cc_start: 0.8941 (t) cc_final: 0.8665 (p) REVERT: B 39 ASP cc_start: 0.8866 (t0) cc_final: 0.8441 (t0) REVERT: H 73 ASP cc_start: 0.8407 (t0) cc_final: 0.7949 (t0) REVERT: L 82 ASP cc_start: 0.9265 (p0) cc_final: 0.9042 (p0) REVERT: L 132 VAL cc_start: 0.9118 (t) cc_final: 0.8900 (t) REVERT: L 192 TYR cc_start: 0.9170 (m-80) cc_final: 0.8966 (m-80) REVERT: L 193 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8484 (t) outliers start: 39 outliers final: 22 residues processed: 222 average time/residue: 0.1758 time to fit residues: 51.5471 Evaluate side-chains 204 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 H residue 2 VAL 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 91 SER Chi-restraints excluded: chain H residue 166 LEU 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 193 THR Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.108942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.088903 restraints weight = 9928.517| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.81 r_work: 0.2816 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1392 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= 0.191 Angle : 0.654 13.128 8398 Z= 0.319 Chirality : 0.045 0.179 961 Planarity : 0.005 0.056 1050 Dihedral : 4.403 21.294 829 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 6.96 % Allowed : 24.44 % 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: 0.19 (0.31), residues: 774 helix: 1.75 (0.33), residues: 255 sheet: 0.65 (0.37), residues: 214 loop : -1.75 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS L 91 PHE 0.009 0.001 PHE H 153 TYR 0.012 0.001 TYR L 49 ARG 0.011 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 291) hydrogen bonds : angle 4.41994 ( 864) SS BOND : bond 0.00399 ( 3) SS BOND : angle 2.36173 ( 6) covalent geometry : bond 0.00460 ( 6168) covalent geometry : angle 0.65073 ( 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 215 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9149 (mt) cc_final: 0.8855 (mt) REVERT: A 180 ARG cc_start: 0.7587 (ptp-170) cc_final: 0.6630 (ptp-170) REVERT: A 183 TYR cc_start: 0.7477 (m-80) cc_final: 0.6862 (m-80) REVERT: A 229 MET cc_start: 0.8748 (ttm) cc_final: 0.8425 (ttt) REVERT: A 254 VAL cc_start: 0.8839 (t) cc_final: 0.8565 (p) REVERT: H 73 ASP cc_start: 0.8364 (t0) cc_final: 0.7922 (t0) REVERT: L 193 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8358 (t) outliers start: 47 outliers final: 39 residues processed: 204 average time/residue: 0.1856 time to fit residues: 51.1021 Evaluate side-chains 199 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 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 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 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 194 CYS 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: 0.0870 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.110813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.091086 restraints weight = 9662.289| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.80 r_work: 0.2869 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1458 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= 0.123 Angle : 0.626 13.140 8398 Z= 0.301 Chirality : 0.043 0.162 961 Planarity : 0.005 0.053 1050 Dihedral : 4.243 20.724 829 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.04 % Allowed : 28.00 % 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 (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: 1.89 (0.33), residues: 254 sheet: 0.67 (0.37), residues: 214 loop : -1.72 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.001 0.000 HIS L 91 PHE 0.008 0.001 PHE A 310 TYR 0.013 0.001 TYR L 49 ARG 0.011 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 291) hydrogen bonds : angle 4.26829 ( 864) SS BOND : bond 0.00486 ( 3) SS BOND : angle 2.24802 ( 6) covalent geometry : bond 0.00283 ( 6168) covalent geometry : angle 0.62365 ( 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 203 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9255 (mt) cc_final: 0.9001 (mt) REVERT: A 180 ARG cc_start: 0.7537 (ptp-170) cc_final: 0.6566 (ptp-170) REVERT: A 183 TYR cc_start: 0.7484 (m-80) cc_final: 0.6862 (m-80) REVERT: A 229 MET cc_start: 0.8784 (ttm) cc_final: 0.8559 (ttt) REVERT: A 254 VAL cc_start: 0.8903 (t) cc_final: 0.8558 (p) REVERT: H 73 ASP cc_start: 0.8394 (t0) cc_final: 0.7935 (t0) REVERT: H 112 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8936 (pm20) REVERT: L 193 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8404 (t) REVERT: L 207 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7986 (mptt) outliers start: 34 outliers final: 25 residues processed: 197 average time/residue: 0.1718 time to fit residues: 44.4573 Evaluate side-chains 195 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 171 THR 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 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 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 L residue 12 SER 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 193 THR Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.111316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.091061 restraints weight = 9707.278| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.82 r_work: 0.2858 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6171 Z= 0.137 Angle : 0.634 13.983 8398 Z= 0.305 Chirality : 0.043 0.150 961 Planarity : 0.005 0.052 1050 Dihedral : 4.241 20.040 829 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.93 % Allowed : 27.41 % 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 (0.30), residues: 774 helix: 1.80 (0.33), residues: 249 sheet: 0.66 (0.37), residues: 216 loop : -1.67 (0.32), residues: 309 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 0.007 0.001 PHE B 23 TYR 0.012 0.001 TYR L 49 ARG 0.009 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 291) hydrogen bonds : angle 4.24776 ( 864) SS BOND : bond 0.00495 ( 3) SS BOND : angle 2.52561 ( 6) covalent geometry : bond 0.00323 ( 6168) covalent geometry : angle 0.63086 ( 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 216 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9207 (mt) cc_final: 0.8954 (mt) REVERT: A 180 ARG cc_start: 0.7556 (ptp-170) cc_final: 0.6529 (ptp-170) REVERT: A 183 TYR cc_start: 0.7416 (m-80) cc_final: 0.6822 (m-80) REVERT: A 254 VAL cc_start: 0.8879 (t) cc_final: 0.8560 (p) REVERT: H 73 ASP cc_start: 0.8418 (t0) cc_final: 0.7893 (t0) REVERT: H 112 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8872 (pm20) REVERT: L 132 VAL cc_start: 0.9059 (t) cc_final: 0.8856 (t) REVERT: L 192 TYR cc_start: 0.9161 (m-80) cc_final: 0.8955 (m-80) REVERT: L 193 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8323 (t) REVERT: L 207 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7931 (mptt) outliers start: 40 outliers final: 30 residues processed: 206 average time/residue: 0.1652 time to fit residues: 45.0876 Evaluate side-chains 203 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 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 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 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 207 LYS Chi-restraints excluded: chain L residue 209 PHE 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: 1.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.112358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.092101 restraints weight = 9693.792| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.83 r_work: 0.2879 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1560 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= 0.124 Angle : 0.634 13.698 8398 Z= 0.304 Chirality : 0.043 0.199 961 Planarity : 0.005 0.051 1050 Dihedral : 4.155 19.323 829 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.19 % Allowed : 28.59 % 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: 0.25 (0.30), residues: 774 helix: 1.82 (0.33), residues: 249 sheet: 0.68 (0.37), residues: 216 loop : -1.65 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 106 HIS 0.002 0.000 HIS L 91 PHE 0.007 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 0.03547 ( 291) hydrogen bonds : angle 4.19778 ( 864) SS BOND : bond 0.00533 ( 3) SS BOND : angle 2.51693 ( 6) covalent geometry : bond 0.00287 ( 6168) covalent geometry : angle 0.63081 ( 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: 35 poor density : 180 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 112 MET cc_start: 0.7748 (mtt) cc_final: 0.7435 (mtt) REVERT: A 165 LEU cc_start: 0.9178 (mt) cc_final: 0.8927 (mt) REVERT: A 180 ARG cc_start: 0.7585 (ptp-170) cc_final: 0.6616 (ptp-170) REVERT: A 183 TYR cc_start: 0.7347 (m-80) cc_final: 0.6792 (m-80) REVERT: A 254 VAL cc_start: 0.8872 (t) cc_final: 0.8565 (p) REVERT: H 13 ARG cc_start: 0.8608 (mmm-85) cc_final: 0.8063 (mmm160) REVERT: H 73 ASP cc_start: 0.8362 (t0) cc_final: 0.7813 (t0) REVERT: H 112 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8524 (pt0) REVERT: L 32 TYR cc_start: 0.9225 (m-10) cc_final: 0.8916 (m-10) REVERT: L 132 VAL cc_start: 0.9026 (t) cc_final: 0.8818 (t) REVERT: L 192 TYR cc_start: 0.9170 (m-80) cc_final: 0.8958 (m-80) REVERT: L 193 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8207 (t) REVERT: L 207 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7822 (mptt) outliers start: 35 outliers final: 28 residues processed: 208 average time/residue: 0.1855 time to fit residues: 51.6518 Evaluate side-chains 209 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 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 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 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 194 CYS 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: 0.8980 chunk 2 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 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 = 0.3307 r_free = 0.3307 target = 0.111868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.092181 restraints weight = 9652.811| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.78 r_work: 0.2876 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1608 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= 0.133 Angle : 0.649 13.782 8398 Z= 0.313 Chirality : 0.043 0.187 961 Planarity : 0.005 0.060 1050 Dihedral : 4.156 19.330 829 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.04 % Allowed : 28.44 % Favored : 66.52 % 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: 0.24 (0.30), residues: 774 helix: 1.80 (0.33), residues: 250 sheet: 0.69 (0.37), residues: 216 loop : -1.69 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.002 0.000 HIS L 91 PHE 0.007 0.001 PHE B 23 TYR 0.023 0.001 TYR H 152 ARG 0.014 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 291) hydrogen bonds : angle 4.22077 ( 864) SS BOND : bond 0.00526 ( 3) SS BOND : angle 2.63964 ( 6) covalent geometry : bond 0.00312 ( 6168) covalent geometry : angle 0.64557 ( 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: 34 poor density : 181 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9216 (mt) cc_final: 0.8961 (mt) REVERT: A 180 ARG cc_start: 0.7555 (ptp-170) cc_final: 0.6554 (ptp-170) REVERT: A 183 TYR cc_start: 0.7395 (m-80) cc_final: 0.6821 (m-80) REVERT: A 229 MET cc_start: 0.8777 (ttm) cc_final: 0.8418 (ttt) REVERT: A 254 VAL cc_start: 0.8924 (t) cc_final: 0.8629 (p) REVERT: H 13 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8110 (mmm160) REVERT: H 73 ASP cc_start: 0.8467 (t0) cc_final: 0.7842 (t0) REVERT: H 112 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8600 (pt0) REVERT: H 182 TYR cc_start: 0.9061 (m-80) cc_final: 0.8623 (m-80) REVERT: L 132 VAL cc_start: 0.9170 (t) cc_final: 0.8961 (t) REVERT: L 192 TYR cc_start: 0.9252 (m-80) cc_final: 0.9045 (m-80) REVERT: L 193 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8370 (t) REVERT: L 207 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7897 (mptt) outliers start: 34 outliers final: 30 residues processed: 208 average time/residue: 0.1585 time to fit residues: 44.1500 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 : 0.685 ------------------------------------------------------------------------------- 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 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 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 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 194 CYS 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: 0.5980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 0.0050 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.113493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.093324 restraints weight = 9732.733| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.84 r_work: 0.2898 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6171 Z= 0.117 Angle : 0.642 14.379 8398 Z= 0.306 Chirality : 0.043 0.198 961 Planarity : 0.005 0.057 1050 Dihedral : 4.088 19.153 829 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.44 % Allowed : 29.33 % 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: 0.27 (0.30), residues: 774 helix: 1.78 (0.33), residues: 250 sheet: 0.75 (0.37), residues: 216 loop : -1.66 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 195 HIS 0.001 0.000 HIS L 91 PHE 0.007 0.001 PHE A 310 TYR 0.019 0.001 TYR H 152 ARG 0.014 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 291) hydrogen bonds : angle 4.15385 ( 864) SS BOND : bond 0.00496 ( 3) SS BOND : angle 2.59659 ( 6) covalent geometry : bond 0.00266 ( 6168) covalent geometry : angle 0.63833 ( 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 213 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9267 (mt) cc_final: 0.9010 (mt) REVERT: A 180 ARG cc_start: 0.7535 (ptp-170) cc_final: 0.6553 (ptp-110) REVERT: A 183 TYR cc_start: 0.7378 (m-80) cc_final: 0.6809 (m-80) REVERT: A 229 MET cc_start: 0.8805 (ttm) cc_final: 0.8483 (ttt) REVERT: A 254 VAL cc_start: 0.8959 (t) cc_final: 0.8713 (p) REVERT: H 13 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8024 (mmm160) REVERT: H 73 ASP cc_start: 0.8361 (t0) cc_final: 0.7712 (t0) REVERT: H 112 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: H 182 TYR cc_start: 0.9051 (m-80) cc_final: 0.8667 (m-80) REVERT: L 4 MET cc_start: 0.8801 (tpp) cc_final: 0.8349 (mmm) REVERT: L 32 TYR cc_start: 0.9229 (m-10) cc_final: 0.8923 (m-10) REVERT: L 193 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8180 (t) REVERT: L 207 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7788 (mptt) outliers start: 30 outliers final: 24 residues processed: 206 average time/residue: 0.1489 time to fit residues: 41.3103 Evaluate side-chains 207 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 20 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 193 THR Chi-restraints excluded: chain L residue 194 CYS 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: 3.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.113061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.092828 restraints weight = 9837.435| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.85 r_work: 0.2885 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1742 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= 0.131 Angle : 0.651 14.414 8398 Z= 0.312 Chirality : 0.043 0.194 961 Planarity : 0.005 0.056 1050 Dihedral : 4.137 19.123 829 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.59 % Allowed : 29.19 % 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: 0.25 (0.30), residues: 774 helix: 1.73 (0.33), residues: 250 sheet: 0.77 (0.37), residues: 216 loop : -1.68 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 148 HIS 0.002 0.000 HIS L 91 PHE 0.007 0.001 PHE A 310 TYR 0.017 0.001 TYR A 69 ARG 0.013 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 291) hydrogen bonds : angle 4.17108 ( 864) SS BOND : bond 0.00450 ( 3) SS BOND : angle 2.62330 ( 6) covalent geometry : bond 0.00307 ( 6168) covalent geometry : angle 0.64770 ( 8392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3499.62 seconds wall clock time: 61 minutes 48.52 seconds (3708.52 seconds total)