Starting phenix.real_space_refine on Fri Aug 22 12:38:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh0_40027/08_2025/8gh0_40027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh0_40027/08_2025/8gh0_40027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gh0_40027/08_2025/8gh0_40027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh0_40027/08_2025/8gh0_40027.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh0_40027/08_2025/8gh0_40027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh0_40027/08_2025/8gh0_40027.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.016 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 9 5.16 5 C 1287 2.51 5 N 326 2.21 5 O 332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 1954 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1939 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'TRP:plan': 2, 'ASN:plan1': 6, 'ARG:plan': 5, 'ASP:plan': 4, 'GLU:plan': 9, 'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 153 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.96, per 1000 atoms: 0.49 Number of scatterers: 1954 At special positions: 0 Unit cell: (55.5328, 85.0346, 65.0775, 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 9 16.00 O 332 8.00 N 326 7.00 C 1287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.04 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 0.23 Conformation dependent library (CDL) restraints added in 151.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'R' and resid 37 through 61 removed outlier: 3.699A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 4.021A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.588A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.637A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.728A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.905A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL R 160 " --> pdb=" O MET R 156 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 181 through 186 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.693A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.992A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.225A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.515A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 161 hydrogen bonds defined for protein. 480 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: 0.24 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 596 1.34 - 1.46: 518 1.46 - 1.58: 878 1.58 - 1.71: 0 1.71 - 1.83: 12 Bond restraints: 2004 Sorted by residual: bond pdb=" CA HIS R 296 " pdb=" C HIS R 296 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.27e-02 6.20e+03 9.02e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C HIS R 296 " pdb=" N VAL R 297 " ideal model delta sigma weight residual 1.335 1.306 0.028 1.26e-02 6.30e+03 5.07e+00 ... (remaining 1999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 2562 1.10 - 2.20: 151 2.20 - 3.30: 32 3.30 - 4.40: 6 4.40 - 5.50: 8 Bond angle restraints: 2759 Sorted by residual: angle pdb=" N THR R 189 " pdb=" CA THR R 189 " pdb=" C THR R 189 " ideal model delta sigma weight residual 111.28 113.69 -2.41 1.09e+00 8.42e-01 4.89e+00 angle pdb=" CA CYS R 191 " pdb=" CB CYS R 191 " pdb=" SG CYS R 191 " ideal model delta sigma weight residual 114.40 119.24 -4.84 2.30e+00 1.89e-01 4.43e+00 angle pdb=" N ASN R 322 " pdb=" CA ASN R 322 " pdb=" C ASN R 322 " ideal model delta sigma weight residual 112.75 115.56 -2.81 1.36e+00 5.41e-01 4.28e+00 angle pdb=" CA TRP R 109 " pdb=" CB TRP R 109 " pdb=" CG TRP R 109 " ideal model delta sigma weight residual 113.60 117.46 -3.86 1.90e+00 2.77e-01 4.12e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.44 117.81 2.63 1.30e+00 5.92e-01 4.10e+00 ... (remaining 2754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 1043 16.85 - 33.70: 77 33.70 - 50.54: 15 50.54 - 67.39: 2 67.39 - 84.24: 2 Dihedral angle restraints: 1139 sinusoidal: 314 harmonic: 825 Sorted by residual: dihedral pdb=" CA ALA R 59 " pdb=" C ALA R 59 " pdb=" N LYS R 60 " pdb=" CA LYS R 60 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA TRP R 99 " pdb=" C TRP R 99 " pdb=" N THR R 100 " pdb=" CA THR R 100 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU R 302 " pdb=" C LEU R 302 " pdb=" N ILE R 303 " pdb=" CA ILE R 303 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 1136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 214 0.033 - 0.067: 93 0.067 - 0.100: 18 0.100 - 0.133: 9 0.133 - 0.167: 2 Chirality restraints: 336 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA HIS R 296 " pdb=" N HIS R 296 " pdb=" C HIS R 296 " pdb=" CB HIS R 296 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CB VAL R 218 " pdb=" CA VAL R 218 " pdb=" CG1 VAL R 218 " pdb=" CG2 VAL R 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 333 not shown) Planarity restraints: 346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 155 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C LEU R 155 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU R 155 " -0.010 2.00e-02 2.50e+03 pdb=" N MET R 156 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 277 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE R 277 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE R 277 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE R 278 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 99 " 0.008 2.00e-02 2.50e+03 7.37e-03 1.36e+00 pdb=" CG TRP R 99 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP R 99 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 99 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP R 99 " -0.000 2.00e-02 2.50e+03 ... (remaining 343 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 760 2.88 - 3.38: 2097 3.38 - 3.89: 3039 3.89 - 4.39: 2998 4.39 - 4.90: 5005 Nonbonded interactions: 13899 Sorted by model distance: nonbonded pdb=" OD1 ASP R 130 " pdb=" N ARG R 131 " model vdw 2.374 3.120 nonbonded pdb=" O ASN R 318 " pdb=" OD1 ASN R 318 " model vdw 2.516 3.040 nonbonded pdb=" O ILE R 58 " pdb=" NE2 GLN R 65 " model vdw 2.556 3.120 nonbonded pdb=" O HIS R 296 " pdb=" O GLN R 299 " model vdw 2.558 3.040 nonbonded pdb=" O ILE R 127 " pdb=" OD1 ASP R 130 " model vdw 2.579 3.040 ... (remaining 13894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.810 Find NCS groups from input model: 0.000 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.004 0.055 2006 Z= 0.233 Angle : 0.655 5.502 2763 Z= 0.377 Chirality : 0.041 0.167 336 Planarity : 0.004 0.027 346 Dihedral : 13.375 84.238 595 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.89 (0.51), residues: 277 helix: 1.34 (0.38), residues: 202 sheet: None (None), residues: 0 loop : -1.47 (0.62), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 228 TYR 0.007 0.001 TYR R 132 PHE 0.016 0.002 PHE R 108 TRP 0.019 0.003 TRP R 99 HIS 0.004 0.002 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 2004) covalent geometry : angle 0.65119 ( 2759) SS BOND : bond 0.00318 ( 2) SS BOND : angle 2.06936 ( 4) hydrogen bonds : bond 0.17925 ( 161) hydrogen bonds : angle 5.93883 ( 480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.074 Fit side-chains REVERT: R 190 CYS cc_start: 0.6395 (t) cc_final: 0.5772 (t) REVERT: R 215 MET cc_start: 0.7844 (mmm) cc_final: 0.7401 (mtt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0446 time to fit residues: 2.2917 Evaluate side-chains 27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121817 restraints weight = 4097.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124329 restraints weight = 2241.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126260 restraints weight = 1404.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127426 restraints weight = 971.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128395 restraints weight = 742.193| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2006 Z= 0.159 Angle : 0.589 5.328 2763 Z= 0.331 Chirality : 0.042 0.159 336 Planarity : 0.004 0.029 346 Dihedral : 5.369 18.780 307 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.63 % Allowed : 16.45 % Favored : 80.92 % 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 aren not related in a simple way. whole: 1.90 (0.53), residues: 277 helix: 1.87 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -0.77 (0.84), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.014 0.001 TYR R 141 PHE 0.009 0.001 PHE R 332 TRP 0.016 0.002 TRP R 158 HIS 0.012 0.003 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2004) covalent geometry : angle 0.58590 ( 2759) SS BOND : bond 0.00102 ( 2) SS BOND : angle 1.59202 ( 4) hydrogen bonds : bond 0.06224 ( 161) hydrogen bonds : angle 4.49105 ( 480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.082 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.0465 time to fit residues: 2.1080 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123164 restraints weight = 4162.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125902 restraints weight = 2278.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127666 restraints weight = 1421.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129107 restraints weight = 997.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129997 restraints weight = 750.490| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2006 Z= 0.139 Angle : 0.548 5.284 2763 Z= 0.307 Chirality : 0.041 0.163 336 Planarity : 0.003 0.026 346 Dihedral : 5.084 17.963 307 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.29 % Allowed : 17.76 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.52), residues: 277 helix: 1.89 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -0.72 (0.83), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.010 0.001 TYR R 141 PHE 0.010 0.001 PHE R 282 TRP 0.015 0.002 TRP R 109 HIS 0.012 0.003 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2004) covalent geometry : angle 0.54557 ( 2759) SS BOND : bond 0.00052 ( 2) SS BOND : angle 1.38731 ( 4) hydrogen bonds : bond 0.05434 ( 161) hydrogen bonds : angle 4.18339 ( 480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: R 131 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8436 (mmm-85) REVERT: R 133 PHE cc_start: 0.8568 (m-10) cc_final: 0.8360 (m-10) outliers start: 5 outliers final: 5 residues processed: 36 average time/residue: 0.0556 time to fit residues: 2.3990 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123746 restraints weight = 4173.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126303 restraints weight = 2281.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128044 restraints weight = 1441.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129276 restraints weight = 1013.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130210 restraints weight = 768.032| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2006 Z= 0.138 Angle : 0.536 5.325 2763 Z= 0.301 Chirality : 0.041 0.163 336 Planarity : 0.003 0.026 346 Dihedral : 4.971 17.709 307 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 6.58 % Allowed : 19.08 % Favored : 74.34 % 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 aren not related in a simple way. whole: 1.89 (0.52), residues: 277 helix: 1.90 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -0.92 (0.80), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 228 TYR 0.008 0.001 TYR R 141 PHE 0.010 0.001 PHE R 282 TRP 0.015 0.002 TRP R 109 HIS 0.012 0.003 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2004) covalent geometry : angle 0.53409 ( 2759) SS BOND : bond 0.00229 ( 2) SS BOND : angle 1.16625 ( 4) hydrogen bonds : bond 0.05383 ( 161) hydrogen bonds : angle 4.12642 ( 480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: R 131 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8461 (mmm-85) REVERT: R 179 GLN cc_start: 0.7863 (tp40) cc_final: 0.7340 (tm-30) REVERT: R 269 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7111 (t70) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.0531 time to fit residues: 2.4874 Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122106 restraints weight = 4232.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124646 restraints weight = 2294.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126400 restraints weight = 1452.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127704 restraints weight = 1015.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128505 restraints weight = 766.041| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2006 Z= 0.148 Angle : 0.541 5.358 2763 Z= 0.304 Chirality : 0.041 0.167 336 Planarity : 0.003 0.027 346 Dihedral : 4.985 17.630 307 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 9.21 % Allowed : 20.39 % Favored : 70.39 % 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 aren not related in a simple way. whole: 1.83 (0.52), residues: 277 helix: 1.88 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.09 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 228 TYR 0.007 0.001 TYR R 199 PHE 0.011 0.001 PHE R 282 TRP 0.016 0.002 TRP R 109 HIS 0.015 0.003 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2004) covalent geometry : angle 0.54122 ( 2759) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.28278 ( 4) hydrogen bonds : bond 0.05607 ( 161) hydrogen bonds : angle 4.18322 ( 480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: R 66 THR cc_start: 0.8790 (m) cc_final: 0.8576 (m) REVERT: R 179 GLN cc_start: 0.7835 (tp40) cc_final: 0.7276 (tm-30) REVERT: R 272 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8782 (tp) outliers start: 14 outliers final: 9 residues processed: 40 average time/residue: 0.0527 time to fit residues: 2.5494 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 269 HIS R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121389 restraints weight = 4144.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123903 restraints weight = 2236.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125614 restraints weight = 1409.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126839 restraints weight = 985.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127461 restraints weight = 749.920| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2006 Z= 0.151 Angle : 0.541 5.375 2763 Z= 0.304 Chirality : 0.041 0.168 336 Planarity : 0.003 0.026 346 Dihedral : 4.995 17.568 307 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 6.58 % Allowed : 24.34 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.52), residues: 277 helix: 1.82 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.99 (0.80), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 228 TYR 0.007 0.001 TYR R 199 PHE 0.012 0.001 PHE R 282 TRP 0.017 0.002 TRP R 109 HIS 0.012 0.003 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2004) covalent geometry : angle 0.54162 ( 2759) SS BOND : bond 0.00086 ( 2) SS BOND : angle 0.13698 ( 4) hydrogen bonds : bond 0.05703 ( 161) hydrogen bonds : angle 4.19390 ( 480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: R 66 THR cc_start: 0.8789 (m) cc_final: 0.8578 (m) REVERT: R 179 GLN cc_start: 0.7827 (tp40) cc_final: 0.7209 (tm-30) REVERT: R 272 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8815 (tp) outliers start: 10 outliers final: 9 residues processed: 38 average time/residue: 0.0544 time to fit residues: 2.4713 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123341 restraints weight = 4113.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125954 restraints weight = 2228.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127746 restraints weight = 1406.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129015 restraints weight = 982.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.129889 restraints weight = 742.599| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2006 Z= 0.130 Angle : 0.511 5.343 2763 Z= 0.287 Chirality : 0.040 0.170 336 Planarity : 0.003 0.025 346 Dihedral : 4.839 17.050 307 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.92 % Allowed : 27.63 % Favored : 66.45 % 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 aren not related in a simple way. whole: 1.92 (0.52), residues: 277 helix: 1.89 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.88 (0.81), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.006 0.001 TYR R 199 PHE 0.012 0.001 PHE R 282 TRP 0.016 0.002 TRP R 109 HIS 0.012 0.003 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 2004) covalent geometry : angle 0.51093 ( 2759) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.33414 ( 4) hydrogen bonds : bond 0.05266 ( 161) hydrogen bonds : angle 4.06079 ( 480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: R 66 THR cc_start: 0.8714 (m) cc_final: 0.8506 (m) REVERT: R 179 GLN cc_start: 0.7749 (tp40) cc_final: 0.7113 (tm-30) REVERT: R 272 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8785 (tp) outliers start: 9 outliers final: 8 residues processed: 41 average time/residue: 0.0511 time to fit residues: 2.5270 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.0040 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122905 restraints weight = 4071.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125438 restraints weight = 2219.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127250 restraints weight = 1411.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128409 restraints weight = 985.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129372 restraints weight = 753.366| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2006 Z= 0.137 Angle : 0.520 5.371 2763 Z= 0.292 Chirality : 0.040 0.170 336 Planarity : 0.003 0.026 346 Dihedral : 4.796 16.925 307 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 6.58 % Allowed : 27.63 % Favored : 65.79 % 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 aren not related in a simple way. whole: 1.91 (0.52), residues: 277 helix: 1.88 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.85 (0.81), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.007 0.001 TYR R 199 PHE 0.012 0.001 PHE R 282 TRP 0.015 0.002 TRP R 109 HIS 0.009 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2004) covalent geometry : angle 0.51999 ( 2759) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.33216 ( 4) hydrogen bonds : bond 0.05287 ( 161) hydrogen bonds : angle 4.06635 ( 480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.078 Fit side-chains REVERT: R 66 THR cc_start: 0.8716 (m) cc_final: 0.8497 (m) REVERT: R 179 GLN cc_start: 0.7739 (tp40) cc_final: 0.7062 (tm-30) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 0.0525 time to fit residues: 2.5399 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122779 restraints weight = 4026.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125237 restraints weight = 2229.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126911 restraints weight = 1427.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128186 restraints weight = 1015.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129044 restraints weight = 770.478| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2006 Z= 0.142 Angle : 0.555 7.001 2763 Z= 0.312 Chirality : 0.041 0.170 336 Planarity : 0.003 0.026 346 Dihedral : 4.834 18.626 307 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 7.24 % Allowed : 26.97 % Favored : 65.79 % 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 aren not related in a simple way. whole: 1.90 (0.52), residues: 277 helix: 1.88 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.90 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.007 0.001 TYR R 199 PHE 0.012 0.001 PHE R 282 TRP 0.015 0.002 TRP R 109 HIS 0.012 0.003 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 2004) covalent geometry : angle 0.55522 ( 2759) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.45908 ( 4) hydrogen bonds : bond 0.05328 ( 161) hydrogen bonds : angle 4.06150 ( 480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.074 Fit side-chains REVERT: R 179 GLN cc_start: 0.7729 (tp40) cc_final: 0.7044 (tm-30) outliers start: 11 outliers final: 10 residues processed: 41 average time/residue: 0.0503 time to fit residues: 2.4927 Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121014 restraints weight = 4134.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123529 restraints weight = 2263.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125165 restraints weight = 1430.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126435 restraints weight = 1017.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127335 restraints weight = 773.833| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2006 Z= 0.151 Angle : 0.564 6.307 2763 Z= 0.318 Chirality : 0.041 0.170 336 Planarity : 0.003 0.026 346 Dihedral : 4.882 18.987 307 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 7.89 % Allowed : 26.32 % Favored : 65.79 % 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 aren not related in a simple way. whole: 1.84 (0.52), residues: 277 helix: 1.87 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.03 (0.77), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.007 0.001 TYR R 199 PHE 0.012 0.001 PHE R 282 TRP 0.015 0.002 TRP R 109 HIS 0.012 0.003 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2004) covalent geometry : angle 0.56406 ( 2759) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.54322 ( 4) hydrogen bonds : bond 0.05540 ( 161) hydrogen bonds : angle 4.07579 ( 480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.075 Fit side-chains REVERT: R 179 GLN cc_start: 0.7730 (tp40) cc_final: 0.7080 (tm-30) outliers start: 12 outliers final: 10 residues processed: 41 average time/residue: 0.0506 time to fit residues: 2.4945 Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121411 restraints weight = 4127.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123899 restraints weight = 2233.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125547 restraints weight = 1416.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126823 restraints weight = 1008.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127782 restraints weight = 767.406| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2006 Z= 0.143 Angle : 0.558 6.034 2763 Z= 0.315 Chirality : 0.041 0.171 336 Planarity : 0.003 0.026 346 Dihedral : 4.838 19.101 307 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 8.55 % Allowed : 26.32 % Favored : 65.13 % 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 aren not related in a simple way. whole: 1.90 (0.52), residues: 277 helix: 1.90 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.99 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.007 0.001 TYR R 199 PHE 0.012 0.001 PHE R 282 TRP 0.016 0.002 TRP R 109 HIS 0.010 0.003 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2004) covalent geometry : angle 0.55775 ( 2759) SS BOND : bond 0.00236 ( 2) SS BOND : angle 0.46047 ( 4) hydrogen bonds : bond 0.05443 ( 161) hydrogen bonds : angle 4.04789 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 594.31 seconds wall clock time: 11 minutes 37.72 seconds (697.72 seconds total)