Starting phenix.real_space_refine on Tue Mar 3 10:50:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wx4_32876/03_2026/7wx4_32876.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wx4_32876/03_2026/7wx4_32876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wx4_32876/03_2026/7wx4_32876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wx4_32876/03_2026/7wx4_32876.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wx4_32876/03_2026/7wx4_32876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wx4_32876/03_2026/7wx4_32876.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 15 5.16 5 C 1256 2.51 5 N 339 2.21 5 O 382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1992 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1887 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain breaks: 3 Chain: "E" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Time building chain proxies: 0.61, per 1000 atoms: 0.31 Number of scatterers: 1992 At special positions: 0 Unit cell: (71.02, 57.24, 81.62, 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 15 16.00 O 382 8.00 N 339 7.00 C 1256 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: 0.16 Conformation dependent library (CDL) restraints added in 79.5 milliseconds 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 488 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 2 sheets defined 48.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 64 through 69 removed outlier: 4.221A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 77 through 93 Processing helix chain 'A' and resid 104 through 119 removed outlier: 4.150A pdb=" N PHE A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.601A pdb=" N LEU A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 163 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.604A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.751A pdb=" N THR A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.790A pdb=" N LEU E 121 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 63 removed outlier: 6.466A pdb=" N VAL A 60 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET A 252 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS A 62 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 249 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 173 removed outlier: 3.685A pdb=" N ALA A 169 " --> pdb=" O VAL A 200 " (cutoff:3.500A) 89 hydrogen bonds defined for protein. 255 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: 0.30 Time building geometry restraints manager: 0.22 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: 659 1.34 - 1.46: 304 1.46 - 1.57: 1026 1.57 - 1.69: 0 1.69 - 1.80: 27 Bond restraints: 2016 Sorted by residual: bond pdb=" CB VAL A 200 " pdb=" CG2 VAL A 200 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 bond pdb=" CG1 ILE A 202 " pdb=" CD1 ILE A 202 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.61e-01 bond pdb=" CB PHE A 108 " pdb=" CG PHE A 108 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.22e-01 bond pdb=" CB ILE A 202 " pdb=" CG2 ILE A 202 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.93e-01 bond pdb=" CA ASN A 206 " pdb=" C ASN A 206 " ideal model delta sigma weight residual 1.526 1.516 0.010 1.15e-02 7.56e+03 7.87e-01 ... (remaining 2011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 2438 0.93 - 1.86: 243 1.86 - 2.79: 28 2.79 - 3.72: 7 3.72 - 4.65: 2 Bond angle restraints: 2718 Sorted by residual: angle pdb=" C MET A 271 " pdb=" N HIS A 272 " pdb=" CA HIS A 272 " ideal model delta sigma weight residual 121.54 125.37 -3.83 1.91e+00 2.74e-01 4.01e+00 angle pdb=" N MET A 123 " pdb=" CA MET A 123 " pdb=" C MET A 123 " ideal model delta sigma weight residual 113.01 110.65 2.36 1.20e+00 6.94e-01 3.86e+00 angle pdb=" C ILE A 202 " pdb=" N ILE A 203 " pdb=" CA ILE A 203 " ideal model delta sigma weight residual 120.34 123.35 -3.01 1.58e+00 4.01e-01 3.64e+00 angle pdb=" NE ARG A 96 " pdb=" CZ ARG A 96 " pdb=" NH1 ARG A 96 " ideal model delta sigma weight residual 121.50 119.73 1.77 1.00e+00 1.00e+00 3.14e+00 angle pdb=" C THR A 334 " pdb=" N PHE A 335 " pdb=" CA PHE A 335 " ideal model delta sigma weight residual 121.42 123.91 -2.49 1.43e+00 4.89e-01 3.04e+00 ... (remaining 2713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 1072 17.55 - 35.09: 121 35.09 - 52.63: 40 52.63 - 70.18: 5 70.18 - 87.72: 3 Dihedral angle restraints: 1241 sinusoidal: 492 harmonic: 749 Sorted by residual: dihedral pdb=" CA LEU A 76 " pdb=" C LEU A 76 " pdb=" N ALA A 77 " pdb=" CA ALA A 77 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB GLU A 182 " pdb=" CG GLU A 182 " pdb=" CD GLU A 182 " pdb=" OE1 GLU A 182 " ideal model delta sinusoidal sigma weight residual 0.00 87.72 -87.72 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N ASN A 260 " pdb=" CA ASN A 260 " pdb=" CB ASN A 260 " pdb=" CG ASN A 260 " ideal model delta sinusoidal sigma weight residual -180.00 -120.25 -59.75 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 164 0.027 - 0.054: 110 0.054 - 0.081: 28 0.081 - 0.108: 18 0.108 - 0.135: 5 Chirality restraints: 325 Sorted by residual: chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL A 101 " pdb=" N VAL A 101 " pdb=" C VAL A 101 " pdb=" CB VAL A 101 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 203 " pdb=" N ILE A 203 " pdb=" C ILE A 203 " pdb=" CB ILE A 203 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 322 not shown) Planarity restraints: 343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 175 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO A 176 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.009 2.00e-02 2.50e+03 7.55e-03 9.99e-01 pdb=" CG PHE A 335 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 261 " 0.014 5.00e-02 4.00e+02 2.15e-02 7.39e-01 pdb=" N PRO A 262 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.012 5.00e-02 4.00e+02 ... (remaining 340 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 335 2.75 - 3.29: 1852 3.29 - 3.83: 3072 3.83 - 4.36: 3457 4.36 - 4.90: 6040 Nonbonded interactions: 14756 Sorted by model distance: nonbonded pdb=" OE2 GLU A 94 " pdb=" NH1 ARG A 96 " model vdw 2.219 3.120 nonbonded pdb=" O SER A 311 " pdb=" OG SER A 311 " model vdw 2.294 3.040 nonbonded pdb=" O SER E 120 " pdb=" OG SER E 120 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP A 232 " pdb=" N SER A 235 " model vdw 2.342 3.120 nonbonded pdb=" N GLU A 49 " pdb=" OE1 GLN A 52 " model vdw 2.356 3.120 ... (remaining 14751 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: 1.130 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.630 Find NCS groups from input model: 0.000 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.006 0.036 2016 Z= 0.258 Angle : 0.589 4.648 2718 Z= 0.346 Chirality : 0.042 0.135 325 Planarity : 0.003 0.025 343 Dihedral : 16.463 87.722 753 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 6.39 % Allowed : 21.00 % Favored : 72.60 % 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: -3.40 (0.48), residues: 250 helix: -0.47 (0.47), residues: 110 sheet: -5.04 (0.61), residues: 37 loop : -3.11 (0.47), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 50 TYR 0.005 0.001 TYR A 259 PHE 0.017 0.002 PHE A 335 TRP 0.002 0.001 TRP A 304 HIS 0.002 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 2016) covalent geometry : angle 0.58902 ( 2718) hydrogen bonds : bond 0.14596 ( 89) hydrogen bonds : angle 7.09645 ( 255) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.116 Fit side-chains REVERT: A 74 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5656 (t70) REVERT: A 174 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8346 (p) REVERT: A 316 ASN cc_start: 0.7358 (t0) cc_final: 0.7120 (t0) REVERT: E 123 MET cc_start: 0.9138 (mmm) cc_final: 0.8166 (tpp) outliers start: 14 outliers final: 9 residues processed: 69 average time/residue: 0.0627 time to fit residues: 4.9222 Evaluate side-chains 64 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116792 restraints weight = 2430.255| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.69 r_work: 0.3248 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2016 Z= 0.163 Angle : 0.495 4.995 2718 Z= 0.265 Chirality : 0.041 0.132 325 Planarity : 0.003 0.027 343 Dihedral : 8.147 57.448 290 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.48 % Allowed : 25.11 % Favored : 69.41 % 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: -2.24 (0.53), residues: 250 helix: 0.48 (0.51), residues: 117 sheet: -4.78 (0.62), residues: 37 loop : -2.53 (0.53), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 50 TYR 0.004 0.001 TYR A 157 PHE 0.017 0.002 PHE A 335 TRP 0.001 0.000 TRP A 304 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 2016) covalent geometry : angle 0.49486 ( 2718) hydrogen bonds : bond 0.04897 ( 89) hydrogen bonds : angle 4.32470 ( 255) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.052 Fit side-chains REVERT: A 90 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7115 (tp30) REVERT: A 123 MET cc_start: 0.8257 (mtm) cc_final: 0.8013 (mmm) REVERT: E 123 MET cc_start: 0.9186 (mmm) cc_final: 0.8080 (tpp) outliers start: 12 outliers final: 11 residues processed: 68 average time/residue: 0.0418 time to fit residues: 3.4074 Evaluate side-chains 62 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.0170 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121101 restraints weight = 2477.315| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.72 r_work: 0.3286 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2016 Z= 0.118 Angle : 0.467 4.928 2718 Z= 0.248 Chirality : 0.039 0.125 325 Planarity : 0.003 0.031 343 Dihedral : 7.098 57.993 282 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.94 % Allowed : 26.03 % Favored : 68.04 % 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: -1.48 (0.55), residues: 250 helix: 0.95 (0.52), residues: 118 sheet: -4.42 (0.61), residues: 37 loop : -1.96 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.004 0.001 TYR A 259 PHE 0.011 0.001 PHE A 335 TRP 0.001 0.000 TRP A 264 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2016) covalent geometry : angle 0.46712 ( 2718) hydrogen bonds : bond 0.04177 ( 89) hydrogen bonds : angle 3.85186 ( 255) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.075 Fit side-chains REVERT: A 90 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: A 193 GLU cc_start: 0.8606 (tm-30) cc_final: 0.7563 (tm-30) REVERT: E 116 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5871 (mt-10) REVERT: E 123 MET cc_start: 0.9151 (mmm) cc_final: 0.8815 (tpp) outliers start: 13 outliers final: 8 residues processed: 61 average time/residue: 0.0394 time to fit residues: 2.9872 Evaluate side-chains 60 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120849 restraints weight = 2489.762| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.74 r_work: 0.3280 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2016 Z= 0.122 Angle : 0.452 4.948 2718 Z= 0.241 Chirality : 0.039 0.152 325 Planarity : 0.003 0.028 343 Dihedral : 6.177 59.643 279 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.94 % Allowed : 26.94 % Favored : 67.12 % 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: -1.03 (0.57), residues: 250 helix: 1.23 (0.52), residues: 118 sheet: -4.24 (0.58), residues: 39 loop : -1.48 (0.66), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.005 0.001 TYR A 259 PHE 0.011 0.001 PHE A 335 TRP 0.001 0.000 TRP A 264 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2016) covalent geometry : angle 0.45230 ( 2718) hydrogen bonds : bond 0.04091 ( 89) hydrogen bonds : angle 3.66355 ( 255) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.087 Fit side-chains REVERT: A 76 LEU cc_start: 0.8402 (mt) cc_final: 0.7975 (mt) REVERT: A 90 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7108 (tp30) REVERT: A 193 GLU cc_start: 0.8652 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 265 GLU cc_start: 0.4940 (OUTLIER) cc_final: 0.4383 (mp0) REVERT: E 123 MET cc_start: 0.9092 (mmm) cc_final: 0.8853 (tpp) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.0426 time to fit residues: 3.3427 Evaluate side-chains 62 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.162262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122518 restraints weight = 2425.197| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.62 r_work: 0.3305 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2016 Z= 0.115 Angle : 0.446 4.954 2718 Z= 0.235 Chirality : 0.039 0.144 325 Planarity : 0.003 0.037 343 Dihedral : 4.691 48.928 275 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.48 % Allowed : 28.77 % Favored : 65.75 % 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: -0.76 (0.57), residues: 250 helix: 1.39 (0.51), residues: 118 sheet: -4.12 (0.57), residues: 39 loop : -1.23 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.005 0.001 TYR A 259 PHE 0.026 0.002 PHE A 188 TRP 0.001 0.000 TRP A 264 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2016) covalent geometry : angle 0.44593 ( 2718) hydrogen bonds : bond 0.03924 ( 89) hydrogen bonds : angle 3.55593 ( 255) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.078 Fit side-chains REVERT: A 76 LEU cc_start: 0.8343 (mt) cc_final: 0.7995 (mt) REVERT: A 90 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: A 193 GLU cc_start: 0.8538 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 265 GLU cc_start: 0.5187 (OUTLIER) cc_final: 0.3937 (mp0) REVERT: E 123 MET cc_start: 0.9095 (mmm) cc_final: 0.8887 (tpp) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.0399 time to fit residues: 3.0716 Evaluate side-chains 64 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.162676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122581 restraints weight = 2415.411| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.70 r_work: 0.3293 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2016 Z= 0.121 Angle : 0.444 4.963 2718 Z= 0.236 Chirality : 0.039 0.139 325 Planarity : 0.003 0.029 343 Dihedral : 4.461 43.463 275 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.94 % Allowed : 29.22 % Favored : 64.84 % 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: -0.52 (0.56), residues: 250 helix: 1.54 (0.51), residues: 118 sheet: -3.92 (0.57), residues: 39 loop : -1.08 (0.66), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.005 0.001 TYR A 259 PHE 0.012 0.001 PHE A 335 TRP 0.001 0.000 TRP A 264 HIS 0.000 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2016) covalent geometry : angle 0.44408 ( 2718) hydrogen bonds : bond 0.03997 ( 89) hydrogen bonds : angle 3.47579 ( 255) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.080 Fit side-chains REVERT: A 76 LEU cc_start: 0.8351 (mt) cc_final: 0.8010 (mt) REVERT: A 90 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7237 (tp30) REVERT: A 193 GLU cc_start: 0.8644 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 265 GLU cc_start: 0.5251 (OUTLIER) cc_final: 0.4705 (mp0) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.0331 time to fit residues: 2.6083 Evaluate side-chains 65 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.162561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122599 restraints weight = 2449.710| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.63 r_work: 0.3300 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2016 Z= 0.124 Angle : 0.447 4.974 2718 Z= 0.237 Chirality : 0.039 0.136 325 Planarity : 0.003 0.029 343 Dihedral : 4.231 37.179 275 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.48 % Allowed : 30.14 % Favored : 64.38 % 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: -0.43 (0.56), residues: 250 helix: 1.55 (0.51), residues: 118 sheet: -3.78 (0.58), residues: 39 loop : -1.00 (0.65), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.006 0.001 TYR A 259 PHE 0.012 0.001 PHE A 335 TRP 0.001 0.000 TRP A 264 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2016) covalent geometry : angle 0.44675 ( 2718) hydrogen bonds : bond 0.03995 ( 89) hydrogen bonds : angle 3.43764 ( 255) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.115 Fit side-chains REVERT: A 76 LEU cc_start: 0.8369 (mt) cc_final: 0.8037 (mt) REVERT: A 90 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: A 128 ASN cc_start: 0.7548 (p0) cc_final: 0.7235 (p0) REVERT: A 193 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 265 GLU cc_start: 0.5426 (OUTLIER) cc_final: 0.4905 (mp0) REVERT: E 123 MET cc_start: 0.8984 (tpp) cc_final: 0.8648 (mmm) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.0361 time to fit residues: 2.7135 Evaluate side-chains 63 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123589 restraints weight = 2483.687| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.65 r_work: 0.3322 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2016 Z= 0.123 Angle : 0.451 4.945 2718 Z= 0.240 Chirality : 0.039 0.135 325 Planarity : 0.003 0.029 343 Dihedral : 4.062 32.810 275 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.85 % Allowed : 28.77 % Favored : 64.38 % 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: -0.35 (0.55), residues: 250 helix: 1.58 (0.51), residues: 118 sheet: -3.63 (0.58), residues: 39 loop : -0.95 (0.64), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 50 TYR 0.006 0.001 TYR A 259 PHE 0.011 0.001 PHE A 335 TRP 0.001 0.000 TRP A 304 HIS 0.000 0.000 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2016) covalent geometry : angle 0.45077 ( 2718) hydrogen bonds : bond 0.03961 ( 89) hydrogen bonds : angle 3.40000 ( 255) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.073 Fit side-chains REVERT: A 76 LEU cc_start: 0.8351 (mt) cc_final: 0.8030 (mt) REVERT: A 90 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7293 (tp30) REVERT: A 193 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7645 (tm-30) REVERT: A 265 GLU cc_start: 0.5463 (OUTLIER) cc_final: 0.4525 (mp0) outliers start: 15 outliers final: 10 residues processed: 61 average time/residue: 0.0415 time to fit residues: 3.1225 Evaluate side-chains 63 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.162947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122901 restraints weight = 2410.524| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.69 r_work: 0.3314 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2016 Z= 0.139 Angle : 0.468 5.000 2718 Z= 0.249 Chirality : 0.039 0.136 325 Planarity : 0.003 0.029 343 Dihedral : 4.121 32.844 275 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.48 % Allowed : 30.59 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.34 (0.55), residues: 250 helix: 1.55 (0.51), residues: 118 sheet: -3.60 (0.59), residues: 39 loop : -0.90 (0.64), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.006 0.001 TYR A 259 PHE 0.012 0.001 PHE A 335 TRP 0.001 0.000 TRP A 264 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2016) covalent geometry : angle 0.46773 ( 2718) hydrogen bonds : bond 0.04189 ( 89) hydrogen bonds : angle 3.41706 ( 255) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.080 Fit side-chains REVERT: A 76 LEU cc_start: 0.8345 (mt) cc_final: 0.8027 (mt) REVERT: A 90 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: A 193 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 265 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.4904 (mp0) outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.0387 time to fit residues: 2.9244 Evaluate side-chains 59 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.163829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123607 restraints weight = 2478.037| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.66 r_work: 0.3320 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2016 Z= 0.131 Angle : 0.469 4.954 2718 Z= 0.250 Chirality : 0.039 0.132 325 Planarity : 0.003 0.029 343 Dihedral : 4.079 32.477 275 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.57 % Allowed : 30.14 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.55), residues: 250 helix: 1.60 (0.51), residues: 118 sheet: -3.44 (0.60), residues: 39 loop : -0.79 (0.63), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 124 TYR 0.008 0.001 TYR A 179 PHE 0.011 0.001 PHE A 335 TRP 0.001 0.000 TRP A 304 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2016) covalent geometry : angle 0.46944 ( 2718) hydrogen bonds : bond 0.04029 ( 89) hydrogen bonds : angle 3.41029 ( 255) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.079 Fit side-chains REVERT: A 76 LEU cc_start: 0.8344 (mt) cc_final: 0.8069 (mt) REVERT: A 90 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: A 193 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 265 GLU cc_start: 0.5313 (OUTLIER) cc_final: 0.4442 (mp0) REVERT: E 123 MET cc_start: 0.8611 (mmt) cc_final: 0.8308 (mmm) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.0403 time to fit residues: 2.9608 Evaluate side-chains 60 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125045 restraints weight = 2414.764| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.71 r_work: 0.3358 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2016 Z= 0.099 Angle : 0.443 5.035 2718 Z= 0.237 Chirality : 0.038 0.124 325 Planarity : 0.003 0.029 343 Dihedral : 3.893 31.878 275 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.65 % Allowed : 31.51 % Favored : 64.84 % 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: 0.07 (0.55), residues: 250 helix: 1.75 (0.51), residues: 118 sheet: -3.12 (0.55), residues: 42 loop : -0.51 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 50 TYR 0.006 0.001 TYR A 179 PHE 0.008 0.001 PHE A 335 TRP 0.001 0.000 TRP A 304 HIS 0.000 0.000 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 2016) covalent geometry : angle 0.44349 ( 2718) hydrogen bonds : bond 0.03378 ( 89) hydrogen bonds : angle 3.29688 ( 255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 671.07 seconds wall clock time: 12 minutes 4.77 seconds (724.77 seconds total)