Starting phenix.real_space_refine on Fri Aug 22 13:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz4_37946/08_2025/8wz4_37946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz4_37946/08_2025/8wz4_37946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wz4_37946/08_2025/8wz4_37946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz4_37946/08_2025/8wz4_37946.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz4_37946/08_2025/8wz4_37946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz4_37946/08_2025/8wz4_37946.cif" } resolution = 3.13 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= -0.001 sd= 0.014 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 16 5.16 5 C 2198 2.51 5 N 564 2.21 5 O 663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3441 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1685 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 925 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Time building chain proxies: 0.85, per 1000 atoms: 0.25 Number of scatterers: 3441 At special positions: 0 Unit cell: (88.692, 82.468, 70.798, 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 16 16.00 O 663 8.00 N 564 7.00 C 2198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.25 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 129.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 27.6% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'C' and resid 73 through 98 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 209 Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.758A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.004A pdb=" N THR H 91 " --> pdb=" O ASN H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 179 through 180 removed outlier: 10.343A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ARG C 49 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY C 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 301 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL C 300 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N MET C 289 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLN C 302 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER C 287 " --> pdb=" O GLN C 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.546A pdb=" N VAL H 18 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 78 " --> pdb=" O GLU H 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.638A pdb=" N THR H 113 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR H 94 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.638A pdb=" N THR H 113 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR H 94 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG H 98 " --> pdb=" O TYR H 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 46 154 hydrogen bonds defined for protein. 417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.32 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 564 1.28 - 1.41: 843 1.41 - 1.54: 2069 1.54 - 1.67: 5 1.67 - 1.81: 24 Bond restraints: 3505 Sorted by residual: bond pdb=" C VAL C 164 " pdb=" O VAL C 164 " ideal model delta sigma weight residual 1.237 1.145 0.092 1.19e-02 7.06e+03 5.99e+01 bond pdb=" N VAL C 164 " pdb=" CA VAL C 164 " ideal model delta sigma weight residual 1.460 1.369 0.091 1.21e-02 6.83e+03 5.65e+01 bond pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.30e-02 5.92e+03 4.82e+01 bond pdb=" N LYS C 166 " pdb=" CA LYS C 166 " ideal model delta sigma weight residual 1.459 1.380 0.079 1.20e-02 6.94e+03 4.35e+01 bond pdb=" C ALA C 170 " pdb=" N LEU C 171 " ideal model delta sigma weight residual 1.331 1.416 -0.084 1.32e-02 5.74e+03 4.09e+01 ... (remaining 3500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 4645 2.53 - 5.05: 84 5.05 - 7.58: 10 7.58 - 10.10: 7 10.10 - 12.63: 1 Bond angle restraints: 4747 Sorted by residual: angle pdb=" N VAL C 164 " pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 110.72 103.29 7.43 1.01e+00 9.80e-01 5.41e+01 angle pdb=" N GLU C 163 " pdb=" CA GLU C 163 " pdb=" C GLU C 163 " ideal model delta sigma weight residual 111.28 119.14 -7.86 1.09e+00 8.42e-01 5.19e+01 angle pdb=" CA LYS C 166 " pdb=" C LYS C 166 " pdb=" N ILE C 167 " ideal model delta sigma weight residual 117.17 124.76 -7.59 1.18e+00 7.18e-01 4.14e+01 angle pdb=" N LEU C 171 " pdb=" CA LEU C 171 " pdb=" C LEU C 171 " ideal model delta sigma weight residual 112.72 105.07 7.65 1.36e+00 5.41e-01 3.16e+01 angle pdb=" CA VAL C 164 " pdb=" C VAL C 164 " pdb=" N ASN C 165 " ideal model delta sigma weight residual 117.28 123.60 -6.32 1.16e+00 7.43e-01 2.97e+01 ... (remaining 4742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.95: 1806 13.95 - 27.91: 222 27.91 - 41.86: 57 41.86 - 55.81: 19 55.81 - 69.77: 5 Dihedral angle restraints: 2109 sinusoidal: 835 harmonic: 1274 Sorted by residual: dihedral pdb=" CB CYS C 155 " pdb=" SG CYS C 155 " pdb=" SG CYS C 290 " pdb=" CB CYS C 290 " ideal model delta sinusoidal sigma weight residual -86.00 -155.77 69.77 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -121.03 35.03 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CA ILE C 291 " pdb=" C ILE C 291 " pdb=" N ILE C 292 " pdb=" CA ILE C 292 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 2106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 529 0.120 - 0.240: 17 0.240 - 0.359: 2 0.359 - 0.479: 1 0.479 - 0.599: 1 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA GLU C 163 " pdb=" N GLU C 163 " pdb=" C GLU C 163 " pdb=" CB GLU C 163 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CA LYS C 166 " pdb=" N LYS C 166 " pdb=" C LYS C 166 " pdb=" CB LYS C 166 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 547 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 170 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ALA C 170 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA C 170 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU C 171 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 168 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LYS C 168 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS C 168 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 169 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 167 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C ILE C 167 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE C 167 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS C 168 " -0.016 2.00e-02 2.50e+03 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 84 2.67 - 3.23: 3256 3.23 - 3.79: 5006 3.79 - 4.34: 6907 4.34 - 4.90: 12143 Nonbonded interactions: 27396 Sorted by model distance: nonbonded pdb=" OH TYR H 99 " pdb=" OH TYR L 96 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR L 49 " pdb=" OD1 ASP L 56 " model vdw 2.302 3.040 nonbonded pdb=" O LEU C 252 " pdb=" NH1 ARG C 282 " model vdw 2.363 3.120 nonbonded pdb=" O THR H 110 " pdb=" OG1 THR H 110 " model vdw 2.369 3.040 ... (remaining 27391 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.730 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 0.216 3509 Z= 0.630 Angle : 0.947 17.640 4755 Z= 0.559 Chirality : 0.062 0.599 550 Planarity : 0.005 0.042 593 Dihedral : 13.979 69.590 1279 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.26 % Allowed : 9.28 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.05 (0.33), residues: 431 helix: -1.06 (0.42), residues: 116 sheet: -2.97 (0.36), residues: 141 loop : -3.46 (0.35), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.018 0.002 TYR H 80 PHE 0.016 0.002 PHE L 91 TRP 0.011 0.002 TRP H 50 HIS 0.004 0.002 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00998 ( 3505) covalent geometry : angle 0.89476 ( 4747) SS BOND : bond 0.10782 ( 4) SS BOND : angle 7.62357 ( 8) hydrogen bonds : bond 0.18201 ( 150) hydrogen bonds : angle 7.47988 ( 417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.122 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.0554 time to fit residues: 7.6314 Evaluate side-chains 72 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124709 restraints weight = 4705.304| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.21 r_work: 0.3398 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3509 Z= 0.157 Angle : 0.608 7.867 4755 Z= 0.320 Chirality : 0.044 0.205 550 Planarity : 0.004 0.030 593 Dihedral : 5.404 48.948 466 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.58 % Allowed : 14.69 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.38), residues: 431 helix: 1.01 (0.49), residues: 116 sheet: -2.33 (0.36), residues: 155 loop : -2.41 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 282 TYR 0.013 0.002 TYR C 299 PHE 0.019 0.002 PHE H 70 TRP 0.013 0.002 TRP H 47 HIS 0.004 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3505) covalent geometry : angle 0.60721 ( 4747) SS BOND : bond 0.00158 ( 4) SS BOND : angle 1.08916 ( 8) hydrogen bonds : bond 0.03466 ( 150) hydrogen bonds : angle 5.03158 ( 417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.146 Fit side-chains REVERT: C 77 LYS cc_start: 0.7707 (tptm) cc_final: 0.7185 (ttpt) REVERT: C 289 MET cc_start: 0.9173 (tpt) cc_final: 0.8670 (tpt) REVERT: H 32 TYR cc_start: 0.8741 (m-80) cc_final: 0.8483 (m-80) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 0.0816 time to fit residues: 7.6260 Evaluate side-chains 71 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121380 restraints weight = 4688.994| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.19 r_work: 0.3351 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3509 Z= 0.182 Angle : 0.619 7.935 4755 Z= 0.324 Chirality : 0.044 0.154 550 Planarity : 0.004 0.033 593 Dihedral : 5.446 44.101 466 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.90 % Allowed : 16.49 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.40), residues: 431 helix: 1.67 (0.49), residues: 116 sheet: -1.89 (0.37), residues: 159 loop : -2.08 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 282 TYR 0.012 0.002 TYR C 299 PHE 0.014 0.002 PHE H 70 TRP 0.011 0.002 TRP H 47 HIS 0.004 0.002 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 3505) covalent geometry : angle 0.61718 ( 4747) SS BOND : bond 0.00344 ( 4) SS BOND : angle 1.32480 ( 8) hydrogen bonds : bond 0.03648 ( 150) hydrogen bonds : angle 4.86804 ( 417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7636 (tptm) cc_final: 0.7180 (ttpt) REVERT: C 80 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7507 (mtmt) REVERT: C 222 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7524 (mt-10) REVERT: C 289 MET cc_start: 0.9248 (tpt) cc_final: 0.8630 (tpt) REVERT: H 19 LYS cc_start: 0.8215 (tttt) cc_final: 0.7749 (ttmt) REVERT: H 32 TYR cc_start: 0.8766 (m-80) cc_final: 0.8416 (m-80) REVERT: L 18 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8189 (m) outliers start: 19 outliers final: 15 residues processed: 83 average time/residue: 0.0588 time to fit residues: 6.0934 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 GLN L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121255 restraints weight = 4669.513| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.18 r_work: 0.3351 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3509 Z= 0.175 Angle : 0.588 7.542 4755 Z= 0.307 Chirality : 0.043 0.150 550 Planarity : 0.003 0.025 593 Dihedral : 5.273 39.159 466 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.90 % Allowed : 18.30 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.41), residues: 431 helix: 1.88 (0.49), residues: 116 sheet: -1.60 (0.38), residues: 162 loop : -2.07 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 282 TYR 0.013 0.002 TYR L 49 PHE 0.012 0.002 PHE H 70 TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 3505) covalent geometry : angle 0.58598 ( 4747) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.30810 ( 8) hydrogen bonds : bond 0.03393 ( 150) hydrogen bonds : angle 4.73807 ( 417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7550 (tptm) cc_final: 0.7218 (ttpt) REVERT: C 80 LYS cc_start: 0.7870 (mmmt) cc_final: 0.7570 (mtmt) REVERT: C 222 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 289 MET cc_start: 0.9291 (tpt) cc_final: 0.8569 (tpt) REVERT: H 32 TYR cc_start: 0.8770 (m-80) cc_final: 0.8362 (m-80) REVERT: H 63 ASP cc_start: 0.7950 (t0) cc_final: 0.7720 (t0) REVERT: H 73 GLU cc_start: 0.7218 (mp0) cc_final: 0.6304 (mp0) REVERT: L 18 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8080 (m) outliers start: 19 outliers final: 14 residues processed: 82 average time/residue: 0.0696 time to fit residues: 7.0388 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121606 restraints weight = 4767.652| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.20 r_work: 0.3354 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3509 Z= 0.156 Angle : 0.570 7.100 4755 Z= 0.297 Chirality : 0.042 0.160 550 Planarity : 0.003 0.026 593 Dihedral : 5.064 33.781 466 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.15 % Allowed : 19.07 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.41), residues: 431 helix: 2.08 (0.49), residues: 116 sheet: -1.40 (0.39), residues: 162 loop : -1.98 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 282 TYR 0.013 0.002 TYR H 80 PHE 0.011 0.002 PHE H 70 TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3505) covalent geometry : angle 0.56833 ( 4747) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.13836 ( 8) hydrogen bonds : bond 0.03216 ( 150) hydrogen bonds : angle 4.58785 ( 417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.099 Fit side-chains REVERT: C 77 LYS cc_start: 0.7545 (tptm) cc_final: 0.7237 (ttpt) REVERT: C 80 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7584 (mtmt) REVERT: C 222 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7507 (mt-10) REVERT: C 289 MET cc_start: 0.9311 (tpt) cc_final: 0.8504 (tpt) REVERT: H 32 TYR cc_start: 0.8753 (m-80) cc_final: 0.8342 (m-80) REVERT: H 63 ASP cc_start: 0.7986 (t0) cc_final: 0.7784 (t0) REVERT: L 18 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8030 (m) outliers start: 20 outliers final: 17 residues processed: 76 average time/residue: 0.0532 time to fit residues: 5.1408 Evaluate side-chains 77 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117538 restraints weight = 4798.482| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.22 r_work: 0.3302 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3509 Z= 0.203 Angle : 0.606 7.498 4755 Z= 0.319 Chirality : 0.043 0.149 550 Planarity : 0.003 0.026 593 Dihedral : 5.208 29.741 466 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.19 % Allowed : 20.10 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.41), residues: 431 helix: 1.96 (0.49), residues: 116 sheet: -1.37 (0.39), residues: 163 loop : -1.96 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 282 TYR 0.017 0.002 TYR H 80 PHE 0.013 0.002 PHE L 91 TRP 0.009 0.002 TRP H 47 HIS 0.004 0.002 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 3505) covalent geometry : angle 0.60456 ( 4747) SS BOND : bond 0.00390 ( 4) SS BOND : angle 1.26029 ( 8) hydrogen bonds : bond 0.03614 ( 150) hydrogen bonds : angle 4.75929 ( 417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.146 Fit side-chains REVERT: C 77 LYS cc_start: 0.7491 (tptm) cc_final: 0.7225 (ttpt) REVERT: C 80 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7699 (mtmt) REVERT: C 222 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7588 (mt-10) REVERT: C 289 MET cc_start: 0.9324 (tpt) cc_final: 0.8452 (tpt) REVERT: H 63 ASP cc_start: 0.8091 (t0) cc_final: 0.7879 (t0) REVERT: L 18 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8033 (m) REVERT: L 81 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7822 (pm20) outliers start: 24 outliers final: 18 residues processed: 78 average time/residue: 0.0520 time to fit residues: 5.1252 Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118581 restraints weight = 4954.981| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.26 r_work: 0.3307 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3509 Z= 0.174 Angle : 0.568 7.112 4755 Z= 0.300 Chirality : 0.043 0.152 550 Planarity : 0.003 0.025 593 Dihedral : 5.018 26.157 466 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.96 % Allowed : 20.36 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.41), residues: 431 helix: 1.99 (0.49), residues: 116 sheet: -1.21 (0.40), residues: 155 loop : -1.84 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 282 TYR 0.016 0.002 TYR H 80 PHE 0.012 0.002 PHE L 91 TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3505) covalent geometry : angle 0.56648 ( 4747) SS BOND : bond 0.00310 ( 4) SS BOND : angle 1.11783 ( 8) hydrogen bonds : bond 0.03357 ( 150) hydrogen bonds : angle 4.64945 ( 417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.127 Fit side-chains REVERT: C 77 LYS cc_start: 0.7426 (tptm) cc_final: 0.7167 (ttpt) REVERT: C 80 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7648 (mtmt) REVERT: C 222 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7560 (mt-10) REVERT: C 289 MET cc_start: 0.9344 (tpt) cc_final: 0.8370 (tpt) REVERT: H 32 TYR cc_start: 0.8754 (m-80) cc_final: 0.8359 (m-80) REVERT: H 63 ASP cc_start: 0.8095 (t0) cc_final: 0.7889 (t0) REVERT: L 18 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8006 (m) REVERT: L 81 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7838 (pm20) outliers start: 27 outliers final: 24 residues processed: 81 average time/residue: 0.0541 time to fit residues: 5.5534 Evaluate side-chains 85 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122473 restraints weight = 4816.210| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.21 r_work: 0.3373 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3509 Z= 0.175 Angle : 0.568 6.942 4755 Z= 0.300 Chirality : 0.042 0.152 550 Planarity : 0.003 0.027 593 Dihedral : 4.940 23.823 466 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 6.70 % Allowed : 20.88 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.41), residues: 431 helix: 1.98 (0.49), residues: 116 sheet: -1.11 (0.40), residues: 157 loop : -1.84 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 282 TYR 0.016 0.002 TYR H 80 PHE 0.012 0.001 PHE L 91 TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 3505) covalent geometry : angle 0.56641 ( 4747) SS BOND : bond 0.00305 ( 4) SS BOND : angle 1.12226 ( 8) hydrogen bonds : bond 0.03383 ( 150) hydrogen bonds : angle 4.63255 ( 417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.135 Fit side-chains REVERT: C 77 LYS cc_start: 0.7405 (tptm) cc_final: 0.7198 (ttpt) REVERT: C 80 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7653 (mtmt) REVERT: C 222 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7581 (mt-10) REVERT: C 289 MET cc_start: 0.9354 (tpt) cc_final: 0.8422 (tpt) REVERT: H 32 TYR cc_start: 0.8754 (m-80) cc_final: 0.8303 (m-80) REVERT: L 18 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.8053 (m) REVERT: L 81 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8026 (pt0) outliers start: 26 outliers final: 21 residues processed: 78 average time/residue: 0.0478 time to fit residues: 4.7178 Evaluate side-chains 80 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122865 restraints weight = 4724.013| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.20 r_work: 0.3377 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3509 Z= 0.170 Angle : 0.569 6.924 4755 Z= 0.301 Chirality : 0.042 0.152 550 Planarity : 0.003 0.027 593 Dihedral : 4.887 23.577 466 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.44 % Allowed : 21.13 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.41), residues: 431 helix: 2.02 (0.49), residues: 116 sheet: -1.01 (0.41), residues: 157 loop : -1.88 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 282 TYR 0.016 0.002 TYR H 80 PHE 0.011 0.001 PHE L 91 TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 3505) covalent geometry : angle 0.56738 ( 4747) SS BOND : bond 0.00305 ( 4) SS BOND : angle 1.09371 ( 8) hydrogen bonds : bond 0.03321 ( 150) hydrogen bonds : angle 4.60310 ( 417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.158 Fit side-chains REVERT: C 77 LYS cc_start: 0.7446 (tptm) cc_final: 0.7244 (ttpt) REVERT: C 222 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7590 (mt-10) REVERT: C 289 MET cc_start: 0.9353 (tpt) cc_final: 0.8428 (tpt) REVERT: H 32 TYR cc_start: 0.8755 (m-80) cc_final: 0.8302 (m-80) REVERT: L 81 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8021 (pt0) outliers start: 25 outliers final: 23 residues processed: 77 average time/residue: 0.0553 time to fit residues: 5.4160 Evaluate side-chains 80 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116112 restraints weight = 4810.314| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.13 r_work: 0.3286 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3509 Z= 0.174 Angle : 0.572 6.853 4755 Z= 0.303 Chirality : 0.042 0.152 550 Planarity : 0.003 0.028 593 Dihedral : 4.885 23.546 466 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.19 % Allowed : 20.62 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.42), residues: 431 helix: 2.00 (0.49), residues: 116 sheet: -0.97 (0.41), residues: 157 loop : -1.88 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 282 TYR 0.016 0.002 TYR H 80 PHE 0.012 0.001 PHE L 91 TRP 0.009 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3505) covalent geometry : angle 0.57054 ( 4747) SS BOND : bond 0.00304 ( 4) SS BOND : angle 1.10788 ( 8) hydrogen bonds : bond 0.03349 ( 150) hydrogen bonds : angle 4.62282 ( 417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.119 Fit side-chains REVERT: C 77 LYS cc_start: 0.7414 (tptm) cc_final: 0.7197 (ttpt) REVERT: C 222 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7492 (mt-10) REVERT: C 289 MET cc_start: 0.9313 (tpt) cc_final: 0.8310 (tpt) REVERT: H 32 TYR cc_start: 0.8726 (m-80) cc_final: 0.8259 (m-80) REVERT: L 18 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.8011 (m) REVERT: L 81 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8025 (pt0) outliers start: 24 outliers final: 21 residues processed: 78 average time/residue: 0.0508 time to fit residues: 5.0008 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116747 restraints weight = 4822.561| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.16 r_work: 0.3294 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3509 Z= 0.155 Angle : 0.551 6.564 4755 Z= 0.292 Chirality : 0.042 0.152 550 Planarity : 0.003 0.028 593 Dihedral : 4.814 23.449 466 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.93 % Allowed : 20.88 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.42), residues: 431 helix: 2.09 (0.49), residues: 116 sheet: -0.81 (0.42), residues: 155 loop : -1.93 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 282 TYR 0.016 0.002 TYR H 80 PHE 0.011 0.002 PHE H 70 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3505) covalent geometry : angle 0.54962 ( 4747) SS BOND : bond 0.00290 ( 4) SS BOND : angle 1.02892 ( 8) hydrogen bonds : bond 0.03191 ( 150) hydrogen bonds : angle 4.54119 ( 417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1099.13 seconds wall clock time: 19 minutes 29.21 seconds (1169.21 seconds total)