Starting phenix.real_space_refine on Tue Feb 3 12:38:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vz0_65475/02_2026/9vz0_65475.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vz0_65475/02_2026/9vz0_65475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vz0_65475/02_2026/9vz0_65475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vz0_65475/02_2026/9vz0_65475.map" model { file = "/net/cci-nas-00/data/ceres_data/9vz0_65475/02_2026/9vz0_65475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vz0_65475/02_2026/9vz0_65475.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.884 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 5 5.16 5 C 1341 2.51 5 N 420 2.21 5 O 437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2203 Number of models: 1 Model: "" Number of chains: 2 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 555 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "I" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1648 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Time building chain proxies: 0.72, per 1000 atoms: 0.33 Number of scatterers: 2203 At special positions: 0 Unit cell: (138.72, 91.12, 111.52, 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 5 16.00 O 437 8.00 N 420 7.00 C 1341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 84.2 milliseconds 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 2 sheets defined 66.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'H' and resid 135 through 201 removed outlier: 4.093A pdb=" N ARG H 139 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER H 162 " --> pdb=" O GLN H 158 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA H 201 " --> pdb=" O LYS H 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 92 Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 175 through 180 Processing helix chain 'I' and resid 188 through 236 removed outlier: 4.162A pdb=" N VAL I 192 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS I 206 " --> pdb=" O LYS I 202 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN I 211 " --> pdb=" O PHE I 207 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS I 212 " --> pdb=" O GLN I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 284 removed outlier: 4.101A pdb=" N THR I 283 " --> pdb=" O ARG I 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 119 through 120 Processing sheet with id=AA2, first strand: chain 'I' and resid 119 through 120 removed outlier: 4.149A pdb=" N GLN I 167 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS I 149 " --> pdb=" O ALA I 165 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ALA I 165 " --> pdb=" O HIS I 149 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 510 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: 0.32 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 683 1.33 - 1.45: 244 1.45 - 1.57: 1281 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 2218 Sorted by residual: bond pdb=" N ASP I 161 " pdb=" CA ASP I 161 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.26e-02 6.30e+03 5.41e+00 bond pdb=" N GLU H 191 " pdb=" CA GLU H 191 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.93e+00 bond pdb=" N THR I 152 " pdb=" CA THR I 152 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.30e-02 5.92e+03 4.73e+00 bond pdb=" N VAL I 175 " pdb=" CA VAL I 175 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.25e-02 6.40e+03 4.34e+00 bond pdb=" N SER I 160 " pdb=" CA SER I 160 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.45e-02 4.76e+03 3.94e+00 ... (remaining 2213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 2866 1.79 - 3.57: 93 3.57 - 5.36: 13 5.36 - 7.14: 1 7.14 - 8.93: 4 Bond angle restraints: 2977 Sorted by residual: angle pdb=" C ASP I 174 " pdb=" N VAL I 175 " pdb=" CA VAL I 175 " ideal model delta sigma weight residual 121.97 113.86 8.11 1.80e+00 3.09e-01 2.03e+01 angle pdb=" N SER I 236 " pdb=" CA SER I 236 " pdb=" C SER I 236 " ideal model delta sigma weight residual 110.80 119.68 -8.88 2.13e+00 2.20e-01 1.74e+01 angle pdb=" CA THR I 152 " pdb=" CB THR I 152 " pdb=" OG1 THR I 152 " ideal model delta sigma weight residual 109.60 105.05 4.55 1.50e+00 4.44e-01 9.19e+00 angle pdb=" CA SER I 160 " pdb=" C SER I 160 " pdb=" O SER I 160 " ideal model delta sigma weight residual 122.14 118.49 3.65 1.24e+00 6.50e-01 8.66e+00 angle pdb=" O VAL I 175 " pdb=" C VAL I 175 " pdb=" N THR I 176 " ideal model delta sigma weight residual 122.57 125.98 -3.41 1.25e+00 6.40e-01 7.45e+00 ... (remaining 2972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 1167 17.79 - 35.57: 175 35.57 - 53.35: 45 53.35 - 71.14: 6 71.14 - 88.92: 5 Dihedral angle restraints: 1398 sinusoidal: 573 harmonic: 825 Sorted by residual: dihedral pdb=" CA ALA I 180 " pdb=" C ALA I 180 " pdb=" N PRO I 181 " pdb=" CA PRO I 181 " ideal model delta harmonic sigma weight residual 180.00 153.02 26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA SER I 236 " pdb=" C SER I 236 " pdb=" N ASP I 237 " pdb=" CA ASP I 237 " ideal model delta harmonic sigma weight residual -180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA MET I 235 " pdb=" C MET I 235 " pdb=" N SER I 236 " pdb=" CA SER I 236 " ideal model delta harmonic sigma weight residual 180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 1395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 213 0.028 - 0.056: 81 0.056 - 0.084: 29 0.084 - 0.112: 8 0.112 - 0.140: 10 Chirality restraints: 341 Sorted by residual: chirality pdb=" CA SER I 236 " pdb=" N SER I 236 " pdb=" C SER I 236 " pdb=" CB SER I 236 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CB VAL I 175 " pdb=" CA VAL I 175 " pdb=" CG1 VAL I 175 " pdb=" CG2 VAL I 175 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE I 144 " pdb=" N ILE I 144 " pdb=" C ILE I 144 " pdb=" CB ILE I 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 338 not shown) Planarity restraints: 401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 180 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.75e+01 pdb=" N PRO I 181 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO I 181 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO I 181 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 137 " -0.017 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" CG PHE H 137 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE H 137 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE H 137 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE H 137 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 137 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 137 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 174 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C ASP I 174 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP I 174 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL I 175 " 0.009 2.00e-02 2.50e+03 ... (remaining 398 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 451 2.78 - 3.31: 2370 3.31 - 3.84: 3531 3.84 - 4.37: 3559 4.37 - 4.90: 6025 Nonbonded interactions: 15936 Sorted by model distance: nonbonded pdb=" O THR I 104 " pdb=" OG1 THR I 104 " model vdw 2.251 3.040 nonbonded pdb=" N ILE I 70 " pdb=" O LEU I 163 " model vdw 2.258 3.120 nonbonded pdb=" O GLN H 166 " pdb=" OG1 THR H 169 " model vdw 2.265 3.040 nonbonded pdb=" NE2 GLN I 167 " pdb=" OD2 ASP I 174 " model vdw 2.268 3.120 nonbonded pdb=" NZ LYS I 91 " pdb=" OG1 THR I 193 " model vdw 2.274 3.120 ... (remaining 15931 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 group one per residue 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: 5.630 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 3.760 Find NCS groups from input model: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 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 : 0.005 0.031 2218 Z= 0.266 Angle : 0.795 8.931 2977 Z= 0.455 Chirality : 0.040 0.140 341 Planarity : 0.007 0.104 401 Dihedral : 18.416 88.920 860 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.85 % Allowed : 24.79 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.47), residues: 283 helix: 2.41 (0.35), residues: 177 sheet: -1.54 (1.22), residues: 16 loop : -2.48 (0.53), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 194 TYR 0.007 0.002 TYR I 267 PHE 0.032 0.002 PHE H 137 HIS 0.004 0.002 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 2218) covalent geometry : angle 0.79455 ( 2977) hydrogen bonds : bond 0.13229 ( 172) hydrogen bonds : angle 4.90435 ( 510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: I 79 ARG cc_start: 0.5867 (mmp80) cc_final: 0.5536 (mpt180) REVERT: I 175 VAL cc_start: 0.6831 (m) cc_final: 0.6261 (t) outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 0.0665 time to fit residues: 2.6013 Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 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 = 0.4090 r_free = 0.4090 target = 0.115495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.103422 restraints weight = 11141.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.104377 restraints weight = 7089.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.105053 restraints weight = 5183.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.105511 restraints weight = 4124.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.105731 restraints weight = 3513.352| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2218 Z= 0.191 Angle : 0.648 9.079 2977 Z= 0.353 Chirality : 0.040 0.153 341 Planarity : 0.005 0.081 401 Dihedral : 4.122 22.768 307 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.70 % Allowed : 22.22 % Favored : 73.08 % 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 are not related in a simple way. whole: 1.70 (0.48), residues: 283 helix: 2.83 (0.34), residues: 177 sheet: -1.09 (1.24), residues: 16 loop : -2.16 (0.56), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 139 TYR 0.005 0.001 TYR H 154 PHE 0.024 0.002 PHE H 137 HIS 0.002 0.001 HIS I 177 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2218) covalent geometry : angle 0.64781 ( 2977) hydrogen bonds : bond 0.09363 ( 172) hydrogen bonds : angle 4.20517 ( 510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 172 ARG cc_start: 0.3043 (OUTLIER) cc_final: 0.1683 (mtt180) REVERT: I 79 ARG cc_start: 0.7565 (mmp80) cc_final: 0.6777 (mpt180) REVERT: I 187 MET cc_start: 0.0813 (tpt) cc_final: 0.0007 (ttt) REVERT: I 240 ASP cc_start: 0.5423 (OUTLIER) cc_final: 0.5125 (t0) REVERT: I 266 LEU cc_start: 0.8682 (tp) cc_final: 0.8466 (tp) outliers start: 11 outliers final: 4 residues processed: 40 average time/residue: 0.0592 time to fit residues: 2.6621 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 240 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.0970 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 overall best weight: 6.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 ASN ** 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 = 0.4078 r_free = 0.4078 target = 0.115228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.103342 restraints weight = 11601.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.104220 restraints weight = 7661.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.104769 restraints weight = 5675.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.105312 restraints weight = 4596.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.105673 restraints weight = 3774.275| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2218 Z= 0.208 Angle : 0.655 8.684 2977 Z= 0.356 Chirality : 0.039 0.148 341 Planarity : 0.006 0.076 401 Dihedral : 4.313 22.413 307 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.27 % Allowed : 23.08 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.48), residues: 283 helix: 2.63 (0.34), residues: 177 sheet: -0.95 (1.28), residues: 16 loop : -2.11 (0.57), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 146 TYR 0.005 0.002 TYR H 154 PHE 0.027 0.002 PHE H 137 HIS 0.003 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 2218) covalent geometry : angle 0.65547 ( 2977) hydrogen bonds : bond 0.09666 ( 172) hydrogen bonds : angle 4.27787 ( 510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 172 ARG cc_start: 0.3411 (OUTLIER) cc_final: 0.2859 (mtt180) REVERT: I 149 HIS cc_start: 0.4383 (OUTLIER) cc_final: 0.2478 (t-90) REVERT: I 187 MET cc_start: 0.1064 (tpt) cc_final: 0.0297 (ttt) REVERT: I 240 ASP cc_start: 0.5295 (OUTLIER) cc_final: 0.5056 (t0) outliers start: 10 outliers final: 6 residues processed: 37 average time/residue: 0.0565 time to fit residues: 2.3982 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 149 HIS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN ** H 189 ASN ** 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 = 0.4104 r_free = 0.4104 target = 0.117001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.105498 restraints weight = 11449.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.106360 restraints weight = 7603.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.106973 restraints weight = 5603.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.107427 restraints weight = 4462.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.107630 restraints weight = 3828.307| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2218 Z= 0.181 Angle : 0.612 9.404 2977 Z= 0.331 Chirality : 0.038 0.154 341 Planarity : 0.005 0.069 401 Dihedral : 3.949 21.576 307 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.70 % Allowed : 27.35 % Favored : 67.95 % 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 are not related in a simple way. whole: 1.94 (0.49), residues: 283 helix: 2.97 (0.35), residues: 177 sheet: -0.63 (1.28), residues: 16 loop : -2.01 (0.58), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 185 TYR 0.005 0.001 TYR H 154 PHE 0.026 0.002 PHE H 137 HIS 0.002 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 2218) covalent geometry : angle 0.61194 ( 2977) hydrogen bonds : bond 0.09044 ( 172) hydrogen bonds : angle 3.95269 ( 510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 172 ARG cc_start: 0.3154 (OUTLIER) cc_final: 0.1782 (mtt180) REVERT: I 86 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7961 (mmm160) REVERT: I 149 HIS cc_start: 0.4278 (OUTLIER) cc_final: 0.2295 (t-90) REVERT: I 177 HIS cc_start: 0.5138 (OUTLIER) cc_final: 0.4126 (t70) REVERT: I 187 MET cc_start: 0.1004 (tpt) cc_final: 0.0199 (ttt) REVERT: I 240 ASP cc_start: 0.5235 (OUTLIER) cc_final: 0.5009 (t0) outliers start: 11 outliers final: 5 residues processed: 38 average time/residue: 0.0596 time to fit residues: 2.5441 Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 HIS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 177 HIS Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 276 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 0.0170 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 1.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN H 167 GLN ** H 189 ASN ** 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 = 0.4126 r_free = 0.4126 target = 0.117906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.106090 restraints weight = 11171.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.106990 restraints weight = 7260.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.107545 restraints weight = 5320.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.108084 restraints weight = 4282.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.108412 restraints weight = 3600.994| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2218 Z= 0.171 Angle : 0.603 9.691 2977 Z= 0.322 Chirality : 0.037 0.163 341 Planarity : 0.004 0.061 401 Dihedral : 3.763 22.133 307 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.85 % Allowed : 27.35 % Favored : 68.80 % 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 are not related in a simple way. whole: 2.30 (0.49), residues: 283 helix: 3.28 (0.34), residues: 177 sheet: -0.33 (1.33), residues: 16 loop : -1.98 (0.58), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 79 TYR 0.004 0.001 TYR H 154 PHE 0.025 0.002 PHE H 137 HIS 0.001 0.000 HIS I 177 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 2218) covalent geometry : angle 0.60324 ( 2977) hydrogen bonds : bond 0.08399 ( 172) hydrogen bonds : angle 3.72297 ( 510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 172 ARG cc_start: 0.2901 (OUTLIER) cc_final: 0.1543 (mtt180) REVERT: I 86 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7991 (mmm160) REVERT: I 91 LYS cc_start: 0.7277 (ptmt) cc_final: 0.6868 (ttpt) REVERT: I 187 MET cc_start: 0.0962 (tpt) cc_final: 0.0232 (ttt) REVERT: I 240 ASP cc_start: 0.5155 (OUTLIER) cc_final: 0.4942 (t0) outliers start: 9 outliers final: 4 residues processed: 36 average time/residue: 0.1073 time to fit residues: 4.2669 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 276 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 0.0470 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 189 ASN ** 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 = 0.4130 r_free = 0.4130 target = 0.118364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.106582 restraints weight = 11417.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.107417 restraints weight = 7836.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.108009 restraints weight = 5833.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.108465 restraints weight = 4735.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.108723 restraints weight = 4039.789| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2218 Z= 0.170 Angle : 0.622 9.628 2977 Z= 0.328 Chirality : 0.038 0.160 341 Planarity : 0.004 0.054 401 Dihedral : 3.784 22.580 307 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.13 % Allowed : 25.64 % Favored : 69.23 % 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 are not related in a simple way. whole: 2.27 (0.49), residues: 283 helix: 3.20 (0.34), residues: 177 sheet: -0.16 (1.33), residues: 16 loop : -1.91 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 282 TYR 0.004 0.001 TYR H 154 PHE 0.025 0.002 PHE H 137 HIS 0.001 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 2218) covalent geometry : angle 0.62150 ( 2977) hydrogen bonds : bond 0.08235 ( 172) hydrogen bonds : angle 3.68615 ( 510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 172 ARG cc_start: 0.3100 (OUTLIER) cc_final: 0.2094 (mtt180) REVERT: I 86 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7739 (mmm160) REVERT: I 177 HIS cc_start: 0.5436 (OUTLIER) cc_final: 0.4186 (t70) REVERT: I 187 MET cc_start: 0.0837 (tpt) cc_final: 0.0231 (ttt) REVERT: I 240 ASP cc_start: 0.4930 (OUTLIER) cc_final: 0.4674 (t0) outliers start: 12 outliers final: 7 residues processed: 40 average time/residue: 0.0632 time to fit residues: 2.8220 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 177 HIS Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 283 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 189 ASN ** 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 = 0.4119 r_free = 0.4119 target = 0.117728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.106023 restraints weight = 11286.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.106883 restraints weight = 7716.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.107494 restraints weight = 5771.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.107938 restraints weight = 4640.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.108179 restraints weight = 3968.097| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2218 Z= 0.179 Angle : 0.658 9.234 2977 Z= 0.339 Chirality : 0.038 0.154 341 Planarity : 0.004 0.048 401 Dihedral : 3.794 22.094 307 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.98 % Allowed : 24.36 % Favored : 69.66 % 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 are not related in a simple way. whole: 2.00 (0.49), residues: 283 helix: 2.93 (0.34), residues: 177 sheet: -0.11 (1.36), residues: 16 loop : -1.91 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 146 TYR 0.004 0.001 TYR H 154 PHE 0.025 0.002 PHE H 137 HIS 0.002 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 2218) covalent geometry : angle 0.65764 ( 2977) hydrogen bonds : bond 0.08428 ( 172) hydrogen bonds : angle 3.83891 ( 510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 169 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8370 (t) REVERT: H 172 ARG cc_start: 0.3055 (OUTLIER) cc_final: 0.2014 (mtt180) REVERT: I 86 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7669 (mtp180) REVERT: I 177 HIS cc_start: 0.5065 (OUTLIER) cc_final: 0.3669 (t70) REVERT: I 187 MET cc_start: 0.0842 (tpt) cc_final: 0.0257 (ttt) REVERT: I 195 LYS cc_start: 0.8539 (tptt) cc_final: 0.8146 (tppt) outliers start: 14 outliers final: 7 residues processed: 41 average time/residue: 0.0538 time to fit residues: 2.5065 Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 177 HIS Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 283 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 40.0000 chunk 22 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 50.0000 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 189 ASN ** 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 = 0.4116 r_free = 0.4116 target = 0.117801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.106330 restraints weight = 11489.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.107112 restraints weight = 7748.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.107723 restraints weight = 5867.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.108071 restraints weight = 4701.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.108387 restraints weight = 4057.033| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2218 Z= 0.190 Angle : 0.664 9.273 2977 Z= 0.348 Chirality : 0.039 0.158 341 Planarity : 0.004 0.046 401 Dihedral : 3.901 19.632 307 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.27 % Allowed : 26.92 % Favored : 68.80 % 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 are not related in a simple way. whole: 1.86 (0.49), residues: 283 helix: 2.74 (0.34), residues: 177 sheet: 0.63 (1.32), residues: 18 loop : -2.02 (0.62), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 146 TYR 0.004 0.001 TYR H 154 PHE 0.025 0.002 PHE H 137 HIS 0.002 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 2218) covalent geometry : angle 0.66426 ( 2977) hydrogen bonds : bond 0.08764 ( 172) hydrogen bonds : angle 4.02358 ( 510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 172 ARG cc_start: 0.2947 (OUTLIER) cc_final: 0.1872 (mtt180) REVERT: I 86 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7660 (mtp180) REVERT: I 177 HIS cc_start: 0.5196 (OUTLIER) cc_final: 0.3808 (t70) REVERT: I 187 MET cc_start: 0.1086 (tpt) cc_final: 0.0409 (ttt) REVERT: I 195 LYS cc_start: 0.8683 (tptt) cc_final: 0.8335 (tppt) outliers start: 10 outliers final: 7 residues processed: 35 average time/residue: 0.0721 time to fit residues: 2.7970 Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 177 HIS Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 283 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 ASN ** H 189 ASN ** 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 = 0.4102 r_free = 0.4102 target = 0.117289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.105966 restraints weight = 11788.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.106816 restraints weight = 7894.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.107353 restraints weight = 5860.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.107816 restraints weight = 4751.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.108040 restraints weight = 4065.678| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2218 Z= 0.206 Angle : 0.707 12.196 2977 Z= 0.368 Chirality : 0.039 0.150 341 Planarity : 0.005 0.048 401 Dihedral : 4.034 18.380 307 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.70 % Allowed : 27.35 % Favored : 67.95 % 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 are not related in a simple way. whole: 1.44 (0.48), residues: 283 helix: 2.37 (0.34), residues: 177 sheet: 0.70 (1.27), residues: 18 loop : -2.12 (0.61), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 185 TYR 0.004 0.001 TYR H 154 PHE 0.024 0.002 PHE H 137 HIS 0.003 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 2218) covalent geometry : angle 0.70658 ( 2977) hydrogen bonds : bond 0.09306 ( 172) hydrogen bonds : angle 4.19647 ( 510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 172 ARG cc_start: 0.3084 (OUTLIER) cc_final: 0.1599 (mtt180) REVERT: I 86 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7738 (mtp180) REVERT: I 149 HIS cc_start: 0.4326 (OUTLIER) cc_final: 0.2440 (t-90) REVERT: I 177 HIS cc_start: 0.5108 (OUTLIER) cc_final: 0.3729 (t70) REVERT: I 187 MET cc_start: 0.1122 (tpt) cc_final: 0.0659 (mtp) outliers start: 11 outliers final: 6 residues processed: 35 average time/residue: 0.0542 time to fit residues: 2.1614 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 HIS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 177 HIS Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 14 optimal weight: 40.0000 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 189 ASN ** 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 = 0.4138 r_free = 0.4138 target = 0.120121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.109025 restraints weight = 12280.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.109910 restraints weight = 8164.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.110536 restraints weight = 5939.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.110832 restraints weight = 4708.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.111242 restraints weight = 4048.707| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2218 Z= 0.182 Angle : 0.691 11.144 2977 Z= 0.354 Chirality : 0.038 0.155 341 Planarity : 0.004 0.045 401 Dihedral : 3.755 19.746 307 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.27 % Allowed : 28.21 % Favored : 67.52 % 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 are not related in a simple way. whole: 1.85 (0.49), residues: 283 helix: 2.72 (0.34), residues: 177 sheet: 0.85 (1.28), residues: 18 loop : -2.04 (0.61), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 139 TYR 0.005 0.001 TYR H 154 PHE 0.025 0.002 PHE H 137 HIS 0.002 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 2218) covalent geometry : angle 0.69111 ( 2977) hydrogen bonds : bond 0.08688 ( 172) hydrogen bonds : angle 3.93866 ( 510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 169 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8310 (t) REVERT: H 172 ARG cc_start: 0.3494 (OUTLIER) cc_final: 0.2679 (mtt180) REVERT: I 86 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7590 (mtp180) REVERT: I 149 HIS cc_start: 0.4859 (OUTLIER) cc_final: 0.2969 (t-90) REVERT: I 177 HIS cc_start: 0.5112 (OUTLIER) cc_final: 0.3667 (t70) REVERT: I 187 MET cc_start: 0.1079 (tpt) cc_final: 0.0339 (ttt) REVERT: I 195 LYS cc_start: 0.8595 (tppt) cc_final: 0.8214 (tppt) outliers start: 10 outliers final: 5 residues processed: 36 average time/residue: 0.0736 time to fit residues: 2.9888 Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 HIS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 177 HIS Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 189 ASN ** 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 = 0.4115 r_free = 0.4115 target = 0.118374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.106993 restraints weight = 11783.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.107830 restraints weight = 7999.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.108452 restraints weight = 5903.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.108902 restraints weight = 4723.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.109072 restraints weight = 4003.391| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2218 Z= 0.207 Angle : 0.714 11.650 2977 Z= 0.370 Chirality : 0.039 0.150 341 Planarity : 0.005 0.047 401 Dihedral : 4.060 18.812 307 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.27 % Allowed : 27.78 % Favored : 67.95 % 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 are not related in a simple way. whole: 1.45 (0.48), residues: 283 helix: 2.38 (0.35), residues: 177 sheet: 0.76 (1.26), residues: 18 loop : -2.14 (0.61), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 139 TYR 0.004 0.002 TYR H 154 PHE 0.024 0.002 PHE H 137 HIS 0.003 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 2218) covalent geometry : angle 0.71443 ( 2977) hydrogen bonds : bond 0.09255 ( 172) hydrogen bonds : angle 4.22269 ( 510) =============================================================================== Job complete usr+sys time: 575.14 seconds wall clock time: 10 minutes 37.56 seconds (637.56 seconds total)