Starting phenix.real_space_refine on Tue Aug 4 11:44:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0z_65521/08_2026/9w0z_65521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0z_65521/08_2026/9w0z_65521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w0z_65521/08_2026/9w0z_65521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0z_65521/08_2026/9w0z_65521.map" model { file = "/net/cci-nas-00/data/ceres_data/9w0z_65521/08_2026/9w0z_65521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0z_65521/08_2026/9w0z_65521.cif" } resolution = 3.3 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= 0.003 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 6 5.16 5 C 978 2.51 5 N 252 2.21 5 O 264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1500 Number of models: 1 Model: "" Number of chains: 1 Chain: "Y" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Restraints were copied for chains: Z, a, b, c, d Time building chain proxies: 0.46, per 1000 atoms: 0.31 Number of scatterers: 1500 At special positions: 0 Unit cell: (72.21, 67.23, 35.69, 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 6 16.00 O 264 8.00 N 252 7.00 C 978 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: 0.10 Conformation dependent library (CDL) restraints added in 57.8 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'a' and resid 12 through 13 removed outlier: 6.417A pdb=" N VAL Y 12 " --> pdb=" O HIS a 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 18 through 20 removed outlier: 6.885A pdb=" N PHE a 19 " --> pdb=" O VAL Y 18 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE Y 19 " --> pdb=" O PHE c 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 24 through 25 removed outlier: 6.503A pdb=" N VAL Y 24 " --> pdb=" O GLY a 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 31 through 32 removed outlier: 6.111A pdb=" N ILE Y 31 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 35 through 36 removed outlier: 7.195A pdb=" N MET Y 35 " --> pdb=" O VAL c 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 40 through 41 removed outlier: 6.392A pdb=" N VAL Y 40 " --> pdb=" O ILE c 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 12 through 13 removed outlier: 6.410A pdb=" N VAL Z 12 " --> pdb=" O HIS b 13 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 18 through 20 removed outlier: 6.885A pdb=" N PHE b 19 " --> pdb=" O VAL Z 18 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N PHE Z 19 " --> pdb=" O PHE d 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 24 through 25 removed outlier: 6.511A pdb=" N VAL Z 24 " --> pdb=" O GLY b 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 31 through 32 removed outlier: 6.114A pdb=" N ILE Z 31 " --> pdb=" O ILE b 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 35 through 36 removed outlier: 7.187A pdb=" N MET Z 35 " --> pdb=" O VAL d 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 40 through 41 removed outlier: 6.406A pdb=" N VAL Z 40 " --> pdb=" O ILE d 41 " (cutoff:3.500A) 12 hydrogen bonds defined for protein. 36 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: 0.10 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 486 1.34 - 1.45: 180 1.45 - 1.56: 846 1.56 - 1.68: 0 1.68 - 1.79: 12 Bond restraints: 1524 Sorted by residual: bond pdb=" CB VAL a 39 " pdb=" CG2 VAL a 39 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL b 39 " pdb=" CG2 VAL b 39 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CB VAL c 39 " pdb=" CG2 VAL c 39 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CB VAL Y 39 " pdb=" CG2 VAL Y 39 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CB VAL Z 39 " pdb=" CG2 VAL Z 39 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 ... (remaining 1519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 1743 0.93 - 1.87: 219 1.87 - 2.80: 63 2.80 - 3.74: 9 3.74 - 4.67: 12 Bond angle restraints: 2046 Sorted by residual: angle pdb=" C VAL d 12 " pdb=" N HIS d 13 " pdb=" CA HIS d 13 " ideal model delta sigma weight residual 121.75 117.08 4.67 1.73e+00 3.34e-01 7.29e+00 angle pdb=" C VAL Y 12 " pdb=" N HIS Y 13 " pdb=" CA HIS Y 13 " ideal model delta sigma weight residual 121.75 117.13 4.62 1.73e+00 3.34e-01 7.14e+00 angle pdb=" C VAL Z 12 " pdb=" N HIS Z 13 " pdb=" CA HIS Z 13 " ideal model delta sigma weight residual 121.75 117.13 4.62 1.73e+00 3.34e-01 7.14e+00 angle pdb=" C VAL b 12 " pdb=" N HIS b 13 " pdb=" CA HIS b 13 " ideal model delta sigma weight residual 121.75 117.13 4.62 1.73e+00 3.34e-01 7.13e+00 angle pdb=" C VAL a 12 " pdb=" N HIS a 13 " pdb=" CA HIS a 13 " ideal model delta sigma weight residual 121.75 117.14 4.61 1.73e+00 3.34e-01 7.11e+00 ... (remaining 2041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.08: 646 9.08 - 18.15: 128 18.15 - 27.22: 24 27.22 - 36.29: 30 36.29 - 45.36: 18 Dihedral angle restraints: 846 sinusoidal: 306 harmonic: 540 Sorted by residual: dihedral pdb=" CA HIS Z 14 " pdb=" C HIS Z 14 " pdb=" N GLN Z 15 " pdb=" CA GLN Z 15 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 dihedral pdb=" CA HIS d 14 " pdb=" C HIS d 14 " pdb=" N GLN d 15 " pdb=" CA GLN d 15 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 dihedral pdb=" CA HIS c 14 " pdb=" C HIS c 14 " pdb=" N GLN c 15 " pdb=" CA GLN c 15 " ideal model delta harmonic sigma weight residual 180.00 164.60 15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 73 0.029 - 0.058: 66 0.058 - 0.087: 40 0.087 - 0.116: 31 0.116 - 0.146: 24 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA HIS Y 14 " pdb=" N HIS Y 14 " pdb=" C HIS Y 14 " pdb=" CB HIS Y 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA HIS d 14 " pdb=" N HIS d 14 " pdb=" C HIS d 14 " pdb=" CB HIS d 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA HIS a 14 " pdb=" N HIS a 14 " pdb=" C HIS a 14 " pdb=" CB HIS a 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 231 not shown) Planarity restraints: 258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS c 14 " -0.003 2.00e-02 2.50e+03 6.50e-03 4.23e-01 pdb=" C HIS c 14 " 0.011 2.00e-02 2.50e+03 pdb=" O HIS c 14 " -0.004 2.00e-02 2.50e+03 pdb=" N GLN c 15 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS Z 14 " -0.003 2.00e-02 2.50e+03 6.48e-03 4.20e-01 pdb=" C HIS Z 14 " 0.011 2.00e-02 2.50e+03 pdb=" O HIS Z 14 " -0.004 2.00e-02 2.50e+03 pdb=" N GLN Z 15 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS d 14 " -0.006 2.00e-02 2.50e+03 5.26e-03 4.15e-01 pdb=" CG HIS d 14 " 0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS d 14 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS d 14 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS d 14 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS d 14 " -0.002 2.00e-02 2.50e+03 ... (remaining 255 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 662 2.93 - 3.42: 1281 3.42 - 3.91: 2337 3.91 - 4.41: 2390 4.41 - 4.90: 4643 Nonbonded interactions: 11313 Sorted by model distance: nonbonded pdb=" OD1 ASN Z 27 " pdb=" N LYS Z 28 " model vdw 2.435 3.120 nonbonded pdb=" OD1 ASN a 27 " pdb=" N LYS a 28 " model vdw 2.435 3.120 nonbonded pdb=" OD1 ASN Y 27 " pdb=" N LYS Y 28 " model vdw 2.436 3.120 nonbonded pdb=" OD1 ASN d 27 " pdb=" N LYS d 28 " model vdw 2.436 3.120 nonbonded pdb=" OD1 ASN c 27 " pdb=" N LYS c 28 " model vdw 2.436 3.120 ... (remaining 11308 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 Found NCS groups: ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 1.110 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.900 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 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 : 0.011 0.037 1524 Z= 0.465 Angle : 0.793 4.670 2046 Z= 0.475 Chirality : 0.070 0.146 234 Planarity : 0.002 0.007 258 Dihedral : 14.203 45.361 510 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.87 (0.44), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.34), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR b 10 PHE 0.004 0.002 PHE Z 19 HIS 0.004 0.002 HIS Z 14 Details of bonding type rmsd/Z covalent geometry : bond 0.01062 / 0.46 ( 1524) covalent geometry : angle 0.79250 / 0.48 ( 2046) hydrogen bonds : bond 0.21877 / 14.04 ( 12) hydrogen bonds : angle 8.65789 / 5.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.048 Fit side-chains REVERT: Y 28 LYS cc_start: 0.8793 (mttt) cc_final: 0.8542 (mtpt) REVERT: a 28 LYS cc_start: 0.8769 (mttt) cc_final: 0.8488 (mtpt) REVERT: b 28 LYS cc_start: 0.8651 (mttt) cc_final: 0.8377 (mtpt) REVERT: d 28 LYS cc_start: 0.8872 (mttt) cc_final: 0.8621 (mtpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0669 time to fit residues: 2.0099 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085544 restraints weight = 2056.783| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.51 r_work: 0.3180 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 1524 Z= 0.084 Angle : 0.487 2.912 2046 Z= 0.273 Chirality : 0.058 0.147 234 Planarity : 0.002 0.007 258 Dihedral : 4.873 13.703 204 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.67 % Allowed : 7.33 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR Z 10 PHE 0.006 0.001 PHE Y 19 HIS 0.002 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.08 ( 1524) covalent geometry : angle 0.48655 / 0.27 ( 2046) hydrogen bonds : bond 0.02251 / 1.36 ( 12) hydrogen bonds : angle 6.05416 / 3.83 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.068 Fit side-chains REVERT: Y 28 LYS cc_start: 0.8775 (mttt) cc_final: 0.8499 (mtpt) REVERT: a 28 LYS cc_start: 0.8775 (mttt) cc_final: 0.8502 (mtpt) REVERT: b 28 LYS cc_start: 0.8629 (mttt) cc_final: 0.8363 (mtpt) REVERT: c 11 GLU cc_start: 0.8376 (tt0) cc_final: 0.7910 (tm-30) REVERT: d 10 TYR cc_start: 0.8398 (m-80) cc_final: 0.8120 (m-80) REVERT: d 28 LYS cc_start: 0.8954 (mttt) cc_final: 0.8595 (mtpp) outliers start: 7 outliers final: 6 residues processed: 34 average time/residue: 0.0749 time to fit residues: 2.8562 Evaluate side-chains 37 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.103311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083902 restraints weight = 2064.601| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.55 r_work: 0.3158 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 1524 Z= 0.116 Angle : 0.464 3.220 2046 Z= 0.267 Chirality : 0.059 0.138 234 Planarity : 0.001 0.007 258 Dihedral : 4.664 13.201 204 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 6.00 % Allowed : 8.67 % Favored : 85.33 % 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: -3.12 (0.53), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR Z 10 PHE 0.004 0.001 PHE Y 19 HIS 0.003 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 1524) covalent geometry : angle 0.46407 / 0.27 ( 2046) hydrogen bonds : bond 0.02568 / 1.59 ( 12) hydrogen bonds : angle 5.74075 / 3.59 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.070 Fit side-chains REVERT: Y 28 LYS cc_start: 0.8769 (mttt) cc_final: 0.8423 (mtpt) REVERT: a 23 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7731 (t0) REVERT: a 28 LYS cc_start: 0.8757 (mttt) cc_final: 0.8490 (mtpt) REVERT: b 28 LYS cc_start: 0.8632 (mttt) cc_final: 0.8369 (mtpt) REVERT: c 11 GLU cc_start: 0.8349 (tt0) cc_final: 0.7850 (tm-30) REVERT: d 10 TYR cc_start: 0.8424 (m-80) cc_final: 0.8139 (m-80) REVERT: d 28 LYS cc_start: 0.8942 (mttt) cc_final: 0.8567 (mtpp) outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 0.0783 time to fit residues: 2.7199 Evaluate side-chains 37 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.106400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086954 restraints weight = 2019.582| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.52 r_work: 0.3211 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1524 Z= 0.080 Angle : 0.417 2.672 2046 Z= 0.243 Chirality : 0.058 0.136 234 Planarity : 0.001 0.007 258 Dihedral : 4.464 12.886 204 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.33 % Allowed : 9.33 % Favored : 85.33 % 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: -2.58 (0.54), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR Z 10 PHE 0.004 0.001 PHE Y 19 HIS 0.002 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 ( 1524) covalent geometry : angle 0.41672 / 0.24 ( 2046) hydrogen bonds : bond 0.02123 / 1.31 ( 12) hydrogen bonds : angle 5.53412 / 3.45 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.058 Fit side-chains REVERT: Y 28 LYS cc_start: 0.8779 (mttt) cc_final: 0.8453 (mtpt) REVERT: a 23 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7777 (t0) REVERT: a 28 LYS cc_start: 0.8763 (mttt) cc_final: 0.8508 (mtpt) REVERT: b 28 LYS cc_start: 0.8611 (mttt) cc_final: 0.8368 (mtpt) REVERT: c 11 GLU cc_start: 0.8332 (tt0) cc_final: 0.7844 (tm-30) REVERT: d 10 TYR cc_start: 0.8372 (m-80) cc_final: 0.8123 (m-80) REVERT: d 28 LYS cc_start: 0.8907 (mttt) cc_final: 0.8550 (mtpp) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 0.0761 time to fit residues: 2.7235 Evaluate side-chains 34 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.106726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087243 restraints weight = 2020.953| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.54 r_work: 0.3218 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1524 Z= 0.077 Angle : 0.428 5.688 2046 Z= 0.242 Chirality : 0.058 0.138 234 Planarity : 0.001 0.007 258 Dihedral : 4.322 12.247 204 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.33 % Allowed : 11.33 % Favored : 85.33 % 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: -2.22 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR Z 10 PHE 0.003 0.001 PHE Z 19 HIS 0.002 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.08 ( 1524) covalent geometry : angle 0.42837 / 0.24 ( 2046) hydrogen bonds : bond 0.01975 / 1.22 ( 12) hydrogen bonds : angle 5.29389 / 3.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.058 Fit side-chains REVERT: Y 22 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8346 (mm-30) REVERT: Y 28 LYS cc_start: 0.8806 (mttt) cc_final: 0.8496 (mtpt) REVERT: a 23 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7878 (t0) REVERT: a 28 LYS cc_start: 0.8777 (mttt) cc_final: 0.8552 (mtpt) REVERT: b 28 LYS cc_start: 0.8618 (mttt) cc_final: 0.8387 (mtpt) REVERT: c 11 GLU cc_start: 0.8265 (tt0) cc_final: 0.7680 (tm-30) REVERT: d 10 TYR cc_start: 0.8381 (m-80) cc_final: 0.8170 (m-80) REVERT: d 28 LYS cc_start: 0.8921 (mttt) cc_final: 0.8570 (mtpp) outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.0778 time to fit residues: 2.5976 Evaluate side-chains 33 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 0.0980 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085117 restraints weight = 2055.424| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.49 r_work: 0.3180 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1524 Z= 0.117 Angle : 0.446 4.627 2046 Z= 0.255 Chirality : 0.059 0.138 234 Planarity : 0.001 0.007 258 Dihedral : 4.388 12.842 204 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.33 % Allowed : 10.67 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.57), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR Z 10 PHE 0.003 0.001 PHE Y 20 HIS 0.003 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 1524) covalent geometry : angle 0.44568 / 0.26 ( 2046) hydrogen bonds : bond 0.02208 / 1.37 ( 12) hydrogen bonds : angle 5.30099 / 3.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.067 Fit side-chains REVERT: Y 28 LYS cc_start: 0.8752 (mttt) cc_final: 0.8428 (mtpt) REVERT: a 23 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7781 (t0) REVERT: a 28 LYS cc_start: 0.8742 (mttt) cc_final: 0.8483 (mtpt) REVERT: b 28 LYS cc_start: 0.8615 (mttt) cc_final: 0.8348 (mtpt) REVERT: c 11 GLU cc_start: 0.8282 (tt0) cc_final: 0.7651 (tm-30) REVERT: d 28 LYS cc_start: 0.8932 (mttt) cc_final: 0.8548 (mtpp) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.0779 time to fit residues: 2.7870 Evaluate side-chains 34 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 0.0270 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.105565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086157 restraints weight = 2002.452| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.51 r_work: 0.3198 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1524 Z= 0.104 Angle : 0.432 4.383 2046 Z= 0.249 Chirality : 0.058 0.137 234 Planarity : 0.001 0.007 258 Dihedral : 4.335 12.999 204 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.00 % Allowed : 10.67 % Favored : 85.33 % 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: -1.79 (0.58), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR Z 10 PHE 0.002 0.001 PHE Y 20 HIS 0.003 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 1524) covalent geometry : angle 0.43244 / 0.25 ( 2046) hydrogen bonds : bond 0.02038 / 1.25 ( 12) hydrogen bonds : angle 5.28956 / 3.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.056 Fit side-chains REVERT: Y 28 LYS cc_start: 0.8757 (mttt) cc_final: 0.8439 (mtpt) REVERT: a 23 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7763 (t0) REVERT: a 28 LYS cc_start: 0.8750 (mttt) cc_final: 0.8494 (mtpt) REVERT: b 28 LYS cc_start: 0.8623 (mttt) cc_final: 0.8351 (mtpt) REVERT: c 11 GLU cc_start: 0.8259 (tt0) cc_final: 0.7620 (tm-30) REVERT: d 28 LYS cc_start: 0.8931 (mttt) cc_final: 0.8549 (mtpp) outliers start: 6 outliers final: 5 residues processed: 33 average time/residue: 0.0747 time to fit residues: 2.7985 Evaluate side-chains 36 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086435 restraints weight = 2058.069| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.53 r_work: 0.3202 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1524 Z= 0.103 Angle : 0.431 4.398 2046 Z= 0.249 Chirality : 0.059 0.137 234 Planarity : 0.001 0.007 258 Dihedral : 4.302 12.895 204 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.00 % Allowed : 10.67 % Favored : 85.33 % 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: -1.66 (0.59), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR Z 10 PHE 0.002 0.001 PHE Z 20 HIS 0.002 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 1524) covalent geometry : angle 0.43060 / 0.25 ( 2046) hydrogen bonds : bond 0.02076 / 1.27 ( 12) hydrogen bonds : angle 5.32461 / 3.22 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.056 Fit side-chains REVERT: Y 28 LYS cc_start: 0.8742 (mttt) cc_final: 0.8432 (mtpt) REVERT: a 23 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7762 (t0) REVERT: a 28 LYS cc_start: 0.8749 (mttt) cc_final: 0.8493 (mtpt) REVERT: b 28 LYS cc_start: 0.8607 (mttt) cc_final: 0.8336 (mtpt) REVERT: c 11 GLU cc_start: 0.8272 (tt0) cc_final: 0.7639 (tm-30) REVERT: d 28 LYS cc_start: 0.8932 (mttt) cc_final: 0.8549 (mtpp) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.0761 time to fit residues: 2.7221 Evaluate side-chains 34 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.0060 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.102411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083485 restraints weight = 2078.643| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.45 r_work: 0.3150 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1524 Z= 0.149 Angle : 0.463 3.787 2046 Z= 0.269 Chirality : 0.060 0.141 234 Planarity : 0.001 0.007 258 Dihedral : 4.480 13.383 204 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.67 % Allowed : 10.67 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.59), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR Z 10 PHE 0.004 0.001 PHE Y 20 HIS 0.003 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 1524) covalent geometry : angle 0.46322 / 0.27 ( 2046) hydrogen bonds : bond 0.02373 / 1.45 ( 12) hydrogen bonds : angle 5.44821 / 3.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.060 Fit side-chains REVERT: Y 28 LYS cc_start: 0.8768 (mttt) cc_final: 0.8449 (mtpt) REVERT: a 23 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7666 (t0) REVERT: a 28 LYS cc_start: 0.8757 (mttt) cc_final: 0.8490 (mtpt) REVERT: b 28 LYS cc_start: 0.8613 (mttt) cc_final: 0.8312 (mtpt) REVERT: c 11 GLU cc_start: 0.8287 (tt0) cc_final: 0.7578 (tm-30) REVERT: d 28 LYS cc_start: 0.8962 (mttt) cc_final: 0.8570 (mtpp) outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.0720 time to fit residues: 2.6514 Evaluate side-chains 35 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain a residue 35 MET Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.104314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084818 restraints weight = 2034.752| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.41 r_work: 0.3147 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1524 Z= 0.147 Angle : 0.465 4.022 2046 Z= 0.269 Chirality : 0.060 0.142 234 Planarity : 0.001 0.007 258 Dihedral : 4.552 13.507 204 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.67 % Allowed : 11.33 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.59), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR Z 10 PHE 0.003 0.001 PHE Z 20 HIS 0.003 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 1524) covalent geometry : angle 0.46487 / 0.27 ( 2046) hydrogen bonds : bond 0.02462 / 1.50 ( 12) hydrogen bonds : angle 5.64886 / 3.45 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.059 Fit side-chains revert: symmetry clash REVERT: Y 28 LYS cc_start: 0.8899 (mttt) cc_final: 0.8591 (mtpt) REVERT: a 23 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7844 (t0) REVERT: a 28 LYS cc_start: 0.8831 (mttt) cc_final: 0.8585 (mtpt) REVERT: b 28 LYS cc_start: 0.8786 (mttt) cc_final: 0.8499 (mtpt) REVERT: d 28 LYS cc_start: 0.9005 (mttt) cc_final: 0.8658 (mtpp) outliers start: 7 outliers final: 6 residues processed: 32 average time/residue: 0.0840 time to fit residues: 2.9836 Evaluate side-chains 34 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain a residue 23 ASP Chi-restraints excluded: chain a residue 35 MET Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.105297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085875 restraints weight = 1991.914| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.38 r_work: 0.3155 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1524 Z= 0.128 Angle : 0.445 3.818 2046 Z= 0.260 Chirality : 0.059 0.138 234 Planarity : 0.001 0.007 258 Dihedral : 4.382 12.907 204 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.67 % Allowed : 11.33 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.59), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR Z 10 PHE 0.003 0.001 PHE Y 20 HIS 0.002 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 1524) covalent geometry : angle 0.44511 / 0.26 ( 2046) hydrogen bonds : bond 0.02186 / 1.33 ( 12) hydrogen bonds : angle 5.46581 / 3.34 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 696.81 seconds wall clock time: 12 minutes 45.67 seconds (765.67 seconds total)