Starting phenix.real_space_refine on Tue Aug 4 14:14:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tuz_56281/08_2026/9tuz_56281.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tuz_56281/08_2026/9tuz_56281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tuz_56281/08_2026/9tuz_56281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tuz_56281/08_2026/9tuz_56281.map" model { file = "/net/cci-nas-00/data/ceres_data/9tuz_56281/08_2026/9tuz_56281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tuz_56281/08_2026/9tuz_56281.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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 20 5.16 5 C 2318 2.51 5 N 614 2.21 5 O 740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3692 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 393 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "B" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1658 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 0.98, per 1000 atoms: 0.27 Number of scatterers: 3692 At special positions: 0 Unit cell: (58.24, 64.064, 98.176, 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 20 16.00 O 740 8.00 N 614 7.00 C 2318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS A 788 " distance=2.03 Simple disulfide: pdb=" SG CYS A 781 " - pdb=" SG CYS A 799 " distance=2.03 Simple disulfide: pdb=" SG CYS A 801 " - pdb=" SG CYS A 813 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 107 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 213 " 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: 0.27 Conformation dependent library (CDL) restraints added in 140.0 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 12 sheets defined 6.8% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.531A pdb=" N ASP B 109 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 110 " --> pdb=" O ALA B 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 106 through 110' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.948A pdb=" N PHE C 102 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 146 removed outlier: 3.625A pdb=" N SER C 146 " --> pdb=" O GLU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 removed outlier: 3.634A pdb=" N HIS C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 786 through 791 Processing sheet with id=AA2, first strand: chain 'A' and resid 805 through 807 Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.385A pdb=" N GLY B 29 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET B 53 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASN B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP B 55 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 3.748A pdb=" N GLY B 165 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR B 202 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 157 through 158 removed outlier: 6.323A pdb=" N TYR B 202 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 177 through 180 removed outlier: 4.722A pdb=" N TYR B 220 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 23 through 26 Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 Processing sheet with id=AB1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 137 removed outlier: 3.819A pdb=" N VAL C 152 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR C 192 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 172 through 174 removed outlier: 4.776A pdb=" N TRP C 167 " --> pdb=" O GLN C 174 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 369 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: 0.53 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1188 1.34 - 1.46: 885 1.46 - 1.58: 1678 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3775 Sorted by residual: bond pdb=" C SER C 84 " pdb=" N GLY C 85 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.80e-01 bond pdb=" CA ALA C 70 " pdb=" CB ALA C 70 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 5.09e-01 bond pdb=" CA LEU C 66 " pdb=" C LEU C 66 " ideal model delta sigma weight residual 1.523 1.518 0.006 8.40e-03 1.42e+04 4.43e-01 bond pdb=" CB CYS B 115 " pdb=" SG CYS B 115 " ideal model delta sigma weight residual 1.808 1.787 0.021 3.30e-02 9.18e+02 4.14e-01 bond pdb=" CA PHE B 172 " pdb=" C PHE B 172 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.26e-02 6.30e+03 3.94e-01 ... (remaining 3770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 5007 1.36 - 2.71: 88 2.71 - 4.07: 24 4.07 - 5.43: 0 5.43 - 6.78: 2 Bond angle restraints: 5121 Sorted by residual: angle pdb=" C LYS C 69 " pdb=" N ALA C 70 " pdb=" CA ALA C 70 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 angle pdb=" N SER B 139 " pdb=" CA SER B 139 " pdb=" C SER B 139 " ideal model delta sigma weight residual 114.31 110.63 3.68 1.29e+00 6.01e-01 8.16e+00 angle pdb=" N THR B 186 " pdb=" CA THR B 186 " pdb=" C THR B 186 " ideal model delta sigma weight residual 114.31 110.64 3.67 1.29e+00 6.01e-01 8.08e+00 angle pdb=" CA LEU B 204 " pdb=" CB LEU B 204 " pdb=" CG LEU B 204 " ideal model delta sigma weight residual 116.30 123.08 -6.78 3.50e+00 8.16e-02 3.75e+00 angle pdb=" CA THR B 186 " pdb=" C THR B 186 " pdb=" N SER B 187 " ideal model delta sigma weight residual 118.81 116.78 2.03 1.15e+00 7.56e-01 3.12e+00 ... (remaining 5116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.67: 2109 12.67 - 25.33: 127 25.33 - 38.00: 27 38.00 - 50.66: 10 50.66 - 63.33: 7 Dihedral angle restraints: 2280 sinusoidal: 887 harmonic: 1393 Sorted by residual: dihedral pdb=" CA CYS A 772 " pdb=" C CYS A 772 " pdb=" N LYS A 773 " pdb=" CA LYS A 773 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP C 111 " pdb=" CB ASP C 111 " pdb=" CG ASP C 111 " pdb=" OD1 ASP C 111 " ideal model delta sinusoidal sigma weight residual -30.00 -87.09 57.09 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" N LEU B 129 " pdb=" CA LEU B 129 " pdb=" CB LEU B 129 " pdb=" CG LEU B 129 " ideal model delta sinusoidal sigma weight residual -180.00 -125.86 -54.14 3 1.50e+01 4.44e-03 9.26e+00 ... (remaining 2277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 343 0.027 - 0.055: 131 0.055 - 0.082: 40 0.082 - 0.110: 43 0.110 - 0.137: 7 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA ILE C 94 " pdb=" N ILE C 94 " pdb=" C ILE C 94 " pdb=" CB ILE C 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE C 67 " pdb=" N ILE C 67 " pdb=" C ILE C 67 " pdb=" CB ILE C 67 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE B 56 " pdb=" N ILE B 56 " pdb=" C ILE B 56 " pdb=" CB ILE B 56 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 561 not shown) Planarity restraints: 661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 174 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO B 175 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 227 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO B 228 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 172 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 173 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " 0.018 5.00e-02 4.00e+02 ... (remaining 658 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 2380 3.07 - 3.53: 3726 3.53 - 3.98: 6062 3.98 - 4.44: 6885 4.44 - 4.90: 11209 Nonbonded interactions: 30262 Sorted by model distance: nonbonded pdb=" N ILE C 48 " pdb=" N SER C 49 " model vdw 2.612 2.560 nonbonded pdb=" N ARG C 127 " pdb=" O ARG C 127 " model vdw 2.646 2.496 nonbonded pdb=" N ALA C 103 " pdb=" O ALA C 103 " model vdw 2.646 2.496 nonbonded pdb=" N SER B 153 " pdb=" O SER B 153 " model vdw 2.655 2.496 nonbonded pdb=" N TYR B 121 " pdb=" O TYR B 121 " model vdw 2.657 2.496 ... (remaining 30257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5441 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 : 0.003 0.021 3782 Z= 0.131 Angle : 0.516 6.782 5135 Z= 0.285 Chirality : 0.041 0.137 564 Planarity : 0.004 0.046 661 Dihedral : 9.786 63.328 1369 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.48 % Allowed : 2.86 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.42), residues: 476 helix: 0.52 (1.49), residues: 14 sheet: 0.74 (0.36), residues: 208 loop : 1.32 (0.46), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.009 0.001 TYR C 110 PHE 0.005 0.001 PHE B 120 TRP 0.009 0.001 TRP C 51 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 3775) covalent geometry : angle 0.51504 / 0.28 ( 5121) SS BOND : bond 0.00291 / 0.15 ( 7) SS BOND : angle 0.85868 / 0.58 ( 14) hydrogen bonds : bond 0.19223 / 11.32 ( 137) hydrogen bonds : angle 10.14304 / 6.76 ( 369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ILE cc_start: 0.6902 (mt) cc_final: 0.6629 (mt) REVERT: B 81 ASP cc_start: 0.7864 (t0) cc_final: 0.7618 (t70) REVERT: C 136 ILE cc_start: 0.7409 (tt) cc_final: 0.6915 (mt) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.0558 time to fit residues: 6.6470 Evaluate side-chains 56 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.205445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.169013 restraints weight = 4807.686| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.43 r_work: 0.3910 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3782 Z= 0.150 Angle : 0.588 7.248 5135 Z= 0.301 Chirality : 0.045 0.148 564 Planarity : 0.005 0.049 661 Dihedral : 4.248 19.627 518 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.43 % Allowed : 10.26 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.42), residues: 476 helix: 0.12 (1.37), residues: 15 sheet: 0.73 (0.37), residues: 215 loop : 1.10 (0.46), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 43 TYR 0.015 0.002 TYR C 106 PHE 0.009 0.001 PHE B 120 TRP 0.015 0.002 TRP B 52 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 3775) covalent geometry : angle 0.58467 / 0.30 ( 5121) SS BOND : bond 0.00367 / 0.19 ( 7) SS BOND : angle 1.30334 / 0.73 ( 14) hydrogen bonds : bond 0.03181 / 1.93 ( 137) hydrogen bonds : angle 6.58073 / 4.36 ( 369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: A 787 MET cc_start: 0.6740 (ppp) cc_final: 0.6220 (ptt) REVERT: B 56 ILE cc_start: 0.7190 (mt) cc_final: 0.6927 (mt) REVERT: B 69 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8321 (p0) REVERT: B 81 ASP cc_start: 0.7255 (t0) cc_final: 0.6969 (t70) REVERT: B 189 VAL cc_start: 0.8607 (t) cc_final: 0.8328 (p) REVERT: C 55 TYR cc_start: 0.6185 (m-80) cc_final: 0.5220 (m-80) REVERT: C 64 ASN cc_start: 0.4999 (m-40) cc_final: 0.4258 (t0) REVERT: C 69 LYS cc_start: 0.6827 (mttp) cc_final: 0.6378 (tptp) REVERT: C 136 ILE cc_start: 0.7604 (tt) cc_final: 0.7043 (mt) outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.0524 time to fit residues: 4.6715 Evaluate side-chains 64 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 30 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.209813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.176693 restraints weight = 4824.025| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.12 r_work: 0.3988 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3782 Z= 0.134 Angle : 0.570 7.129 5135 Z= 0.284 Chirality : 0.043 0.147 564 Planarity : 0.005 0.045 661 Dihedral : 4.167 17.503 518 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.15 % Allowed : 11.93 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.42), residues: 476 helix: -0.23 (1.41), residues: 15 sheet: 0.76 (0.36), residues: 215 loop : 1.06 (0.46), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 807 TYR 0.020 0.002 TYR C 192 PHE 0.013 0.001 PHE C 90 TRP 0.012 0.001 TRP B 52 HIS 0.002 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 3775) covalent geometry : angle 0.56664 / 0.28 ( 5121) SS BOND : bond 0.00304 / 0.16 ( 7) SS BOND : angle 1.29771 / 0.77 ( 14) hydrogen bonds : bond 0.02600 / 1.61 ( 137) hydrogen bonds : angle 6.15193 / 4.06 ( 369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7116 (mt) cc_final: 0.6875 (mt) REVERT: B 189 VAL cc_start: 0.8764 (t) cc_final: 0.8492 (p) REVERT: B 191 THR cc_start: 0.8012 (m) cc_final: 0.7613 (p) REVERT: C 55 TYR cc_start: 0.6477 (m-80) cc_final: 0.5569 (m-80) REVERT: C 64 ASN cc_start: 0.5093 (m-40) cc_final: 0.4374 (t0) REVERT: C 69 LYS cc_start: 0.7327 (mttp) cc_final: 0.6966 (tptp) REVERT: C 73 LEU cc_start: 0.7774 (tt) cc_final: 0.7289 (mt) REVERT: C 136 ILE cc_start: 0.7625 (tt) cc_final: 0.7161 (mt) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.0479 time to fit residues: 4.3907 Evaluate side-chains 66 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 GLN C 166 GLN C 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.201519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.169551 restraints weight = 4824.962| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.18 r_work: 0.3916 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3782 Z= 0.217 Angle : 0.651 7.832 5135 Z= 0.332 Chirality : 0.046 0.157 564 Planarity : 0.005 0.056 661 Dihedral : 4.867 18.067 518 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.10 % Allowed : 12.41 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.42), residues: 476 helix: -0.64 (1.38), residues: 15 sheet: 0.70 (0.36), residues: 209 loop : 0.74 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 807 TYR 0.026 0.003 TYR C 192 PHE 0.014 0.003 PHE C 117 TRP 0.016 0.002 TRP B 52 HIS 0.004 0.002 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 3775) covalent geometry : angle 0.64739 / 0.33 ( 5121) SS BOND : bond 0.00510 / 0.26 ( 7) SS BOND : angle 1.47775 / 0.90 ( 14) hydrogen bonds : bond 0.03175 / 1.96 ( 137) hydrogen bonds : angle 6.31482 / 4.19 ( 369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: B 21 VAL cc_start: 0.1732 (OUTLIER) cc_final: 0.1502 (p) REVERT: B 56 ILE cc_start: 0.7181 (mt) cc_final: 0.6941 (mt) REVERT: B 171 TYR cc_start: 0.7259 (p90) cc_final: 0.6912 (p90) REVERT: B 191 THR cc_start: 0.8275 (m) cc_final: 0.8030 (p) REVERT: B 223 ASN cc_start: 0.4039 (OUTLIER) cc_final: 0.3639 (m-40) REVERT: C 69 LYS cc_start: 0.7427 (mttp) cc_final: 0.6954 (tptp) REVERT: C 73 LEU cc_start: 0.8142 (tt) cc_final: 0.7647 (mt) REVERT: C 91 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7704 (p) REVERT: C 136 ILE cc_start: 0.7666 (tt) cc_final: 0.7209 (mt) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.0571 time to fit residues: 5.8438 Evaluate side-chains 71 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 140 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.201193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.170503 restraints weight = 4840.589| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.57 r_work: 0.3879 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3782 Z= 0.164 Angle : 0.603 7.869 5135 Z= 0.305 Chirality : 0.044 0.144 564 Planarity : 0.004 0.056 661 Dihedral : 4.659 16.997 518 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.34 % Allowed : 15.27 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.41), residues: 476 helix: -1.09 (1.23), residues: 15 sheet: 0.61 (0.36), residues: 212 loop : 0.49 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 807 TYR 0.023 0.002 TYR C 192 PHE 0.011 0.002 PHE B 120 TRP 0.012 0.002 TRP B 52 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 3775) covalent geometry : angle 0.60042 / 0.30 ( 5121) SS BOND : bond 0.00402 / 0.20 ( 7) SS BOND : angle 1.22585 / 0.83 ( 14) hydrogen bonds : bond 0.02827 / 1.75 ( 137) hydrogen bonds : angle 6.03805 / 4.02 ( 369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7158 (mt) cc_final: 0.6883 (mt) REVERT: B 191 THR cc_start: 0.8315 (m) cc_final: 0.8082 (p) REVERT: C 29 THR cc_start: 0.7839 (p) cc_final: 0.7612 (t) REVERT: C 64 ASN cc_start: 0.4926 (m-40) cc_final: 0.4045 (t0) REVERT: C 69 LYS cc_start: 0.7311 (mttp) cc_final: 0.6861 (tptp) REVERT: C 73 LEU cc_start: 0.8047 (tt) cc_final: 0.7561 (mt) REVERT: C 136 ILE cc_start: 0.7636 (tt) cc_final: 0.7203 (mt) outliers start: 14 outliers final: 12 residues processed: 72 average time/residue: 0.0361 time to fit residues: 3.4412 Evaluate side-chains 69 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 140 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN B 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.202964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.168094 restraints weight = 4840.697| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.35 r_work: 0.3910 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3782 Z= 0.129 Angle : 0.575 7.951 5135 Z= 0.289 Chirality : 0.044 0.143 564 Planarity : 0.004 0.049 661 Dihedral : 4.448 15.975 518 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.86 % Allowed : 16.47 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.41), residues: 476 helix: -0.96 (1.30), residues: 15 sheet: 0.67 (0.36), residues: 216 loop : 0.56 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 807 TYR 0.011 0.002 TYR C 192 PHE 0.011 0.002 PHE B 120 TRP 0.010 0.001 TRP B 52 HIS 0.002 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 3775) covalent geometry : angle 0.57352 / 0.29 ( 5121) SS BOND : bond 0.00305 / 0.16 ( 7) SS BOND : angle 0.96742 / 0.69 ( 14) hydrogen bonds : bond 0.02540 / 1.59 ( 137) hydrogen bonds : angle 5.69393 / 3.78 ( 369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.080 Fit side-chains REVERT: B 56 ILE cc_start: 0.7089 (mt) cc_final: 0.6811 (mt) REVERT: B 171 TYR cc_start: 0.7224 (p90) cc_final: 0.6868 (p90) REVERT: B 191 THR cc_start: 0.8390 (m) cc_final: 0.8176 (p) REVERT: C 69 LYS cc_start: 0.7237 (mttp) cc_final: 0.6735 (tptp) REVERT: C 73 LEU cc_start: 0.7965 (tt) cc_final: 0.7495 (mt) REVERT: C 136 ILE cc_start: 0.7712 (tt) cc_final: 0.7279 (mt) REVERT: C 145 LYS cc_start: 0.7249 (mmmt) cc_final: 0.6820 (mmtt) outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.0379 time to fit residues: 3.3745 Evaluate side-chains 62 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 140 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 GLN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.206437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.175411 restraints weight = 4865.546| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.66 r_work: 0.3946 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3782 Z= 0.102 Angle : 0.550 8.406 5135 Z= 0.275 Chirality : 0.043 0.146 564 Planarity : 0.004 0.045 661 Dihedral : 4.220 14.913 518 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.86 % Allowed : 16.95 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.42), residues: 476 helix: -0.72 (1.36), residues: 15 sheet: 0.71 (0.36), residues: 216 loop : 0.71 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 807 TYR 0.015 0.001 TYR B 127 PHE 0.008 0.001 PHE B 120 TRP 0.008 0.001 TRP B 180 HIS 0.001 0.000 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 3775) covalent geometry : angle 0.54989 / 0.27 ( 5121) SS BOND : bond 0.00174 / 0.09 ( 7) SS BOND : angle 0.70936 / 0.58 ( 14) hydrogen bonds : bond 0.02329 / 1.44 ( 137) hydrogen bonds : angle 5.37464 / 3.56 ( 369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7008 (mt) cc_final: 0.6718 (mt) REVERT: B 143 LYS cc_start: 0.6977 (mtpp) cc_final: 0.6216 (tttt) REVERT: B 171 TYR cc_start: 0.7294 (p90) cc_final: 0.6956 (p90) REVERT: C 69 LYS cc_start: 0.7312 (mttp) cc_final: 0.6890 (tptp) REVERT: C 73 LEU cc_start: 0.7866 (tt) cc_final: 0.7404 (mt) REVERT: C 136 ILE cc_start: 0.7623 (tt) cc_final: 0.7225 (mt) REVERT: C 141 ASP cc_start: 0.8193 (t0) cc_final: 0.7606 (t0) REVERT: C 145 LYS cc_start: 0.7306 (mmmt) cc_final: 0.6804 (mmtt) outliers start: 12 outliers final: 12 residues processed: 69 average time/residue: 0.0366 time to fit residues: 3.3211 Evaluate side-chains 70 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.203604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.172739 restraints weight = 4832.151| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.58 r_work: 0.3905 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3782 Z= 0.135 Angle : 0.576 9.062 5135 Z= 0.285 Chirality : 0.044 0.140 564 Planarity : 0.004 0.044 661 Dihedral : 4.306 14.101 518 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.82 % Allowed : 16.71 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.41), residues: 476 helix: -0.82 (1.32), residues: 15 sheet: 0.63 (0.37), residues: 210 loop : 0.58 (0.44), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 807 TYR 0.014 0.002 TYR C 192 PHE 0.010 0.002 PHE B 120 TRP 0.010 0.001 TRP B 52 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 3775) covalent geometry : angle 0.57495 / 0.28 ( 5121) SS BOND : bond 0.00286 / 0.14 ( 7) SS BOND : angle 0.90762 / 0.62 ( 14) hydrogen bonds : bond 0.02509 / 1.57 ( 137) hydrogen bonds : angle 5.39480 / 3.57 ( 369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.130 Fit side-chains REVERT: B 56 ILE cc_start: 0.7036 (mt) cc_final: 0.6764 (mt) REVERT: B 143 LYS cc_start: 0.7163 (mtpp) cc_final: 0.6328 (tttt) REVERT: C 69 LYS cc_start: 0.7309 (mttp) cc_final: 0.6929 (tptp) REVERT: C 73 LEU cc_start: 0.7954 (tt) cc_final: 0.7489 (mt) REVERT: C 136 ILE cc_start: 0.7669 (tt) cc_final: 0.7293 (mt) outliers start: 16 outliers final: 15 residues processed: 72 average time/residue: 0.0546 time to fit residues: 5.0438 Evaluate side-chains 72 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 140 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.206569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.176361 restraints weight = 4815.604| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 3.00 r_work: 0.3937 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3782 Z= 0.112 Angle : 0.572 9.205 5135 Z= 0.284 Chirality : 0.044 0.140 564 Planarity : 0.004 0.044 661 Dihedral : 4.197 13.965 518 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.30 % Allowed : 16.23 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.41), residues: 476 helix: -0.76 (1.38), residues: 15 sheet: 0.66 (0.37), residues: 210 loop : 0.61 (0.44), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 161 TYR 0.031 0.002 TYR C 192 PHE 0.008 0.001 PHE B 120 TRP 0.014 0.001 TRP B 180 HIS 0.001 0.000 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 3775) covalent geometry : angle 0.57197 / 0.28 ( 5121) SS BOND : bond 0.00218 / 0.11 ( 7) SS BOND : angle 0.72259 / 0.54 ( 14) hydrogen bonds : bond 0.02284 / 1.43 ( 137) hydrogen bonds : angle 5.20469 / 3.44 ( 369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.126 Fit side-chains REVERT: B 56 ILE cc_start: 0.6986 (mt) cc_final: 0.6716 (mt) REVERT: B 143 LYS cc_start: 0.7141 (mtpp) cc_final: 0.6393 (tttt) REVERT: C 64 ASN cc_start: 0.4676 (m-40) cc_final: 0.3894 (t0) REVERT: C 69 LYS cc_start: 0.7313 (mttp) cc_final: 0.6960 (tptp) REVERT: C 73 LEU cc_start: 0.7864 (tt) cc_final: 0.7392 (mt) REVERT: C 136 ILE cc_start: 0.7664 (tt) cc_final: 0.7309 (mt) REVERT: C 141 ASP cc_start: 0.8158 (t0) cc_final: 0.7938 (t0) REVERT: C 145 LYS cc_start: 0.7445 (mmmt) cc_final: 0.6976 (mmtt) outliers start: 18 outliers final: 16 residues processed: 72 average time/residue: 0.0600 time to fit residues: 5.4395 Evaluate side-chains 74 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.204268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.173761 restraints weight = 4881.219| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.03 r_work: 0.3909 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3782 Z= 0.139 Angle : 0.595 9.704 5135 Z= 0.296 Chirality : 0.044 0.142 564 Planarity : 0.004 0.044 661 Dihedral : 4.376 14.799 518 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.82 % Allowed : 16.47 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.41), residues: 476 helix: -1.06 (1.27), residues: 15 sheet: 0.60 (0.37), residues: 206 loop : 0.42 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 807 TYR 0.029 0.002 TYR C 192 PHE 0.012 0.002 PHE B 120 TRP 0.017 0.002 TRP B 180 HIS 0.002 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 3775) covalent geometry : angle 0.59405 / 0.30 ( 5121) SS BOND : bond 0.00309 / 0.16 ( 7) SS BOND : angle 0.94772 / 0.64 ( 14) hydrogen bonds : bond 0.02437 / 1.54 ( 137) hydrogen bonds : angle 5.30495 / 3.50 ( 369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.137 Fit side-chains REVERT: B 56 ILE cc_start: 0.7090 (mt) cc_final: 0.6784 (mt) REVERT: B 143 LYS cc_start: 0.7113 (mtpp) cc_final: 0.6325 (tttt) REVERT: C 69 LYS cc_start: 0.7326 (mttp) cc_final: 0.6915 (tptp) REVERT: C 73 LEU cc_start: 0.7912 (tt) cc_final: 0.7419 (mp) REVERT: C 136 ILE cc_start: 0.7711 (tt) cc_final: 0.7354 (mt) REVERT: C 141 ASP cc_start: 0.8122 (t0) cc_final: 0.7861 (t0) REVERT: C 145 LYS cc_start: 0.7478 (mmmt) cc_final: 0.7003 (mmtt) outliers start: 16 outliers final: 15 residues processed: 67 average time/residue: 0.0395 time to fit residues: 3.4970 Evaluate side-chains 69 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.202235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170072 restraints weight = 4827.150| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.82 r_work: 0.3885 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3782 Z= 0.125 Angle : 0.597 13.398 5135 Z= 0.292 Chirality : 0.044 0.139 564 Planarity : 0.004 0.044 661 Dihedral : 4.342 14.839 518 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.58 % Allowed : 16.71 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.41), residues: 476 helix: -1.18 (1.22), residues: 15 sheet: 0.56 (0.37), residues: 206 loop : 0.37 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 161 TYR 0.027 0.002 TYR C 192 PHE 0.011 0.002 PHE C 158 TRP 0.020 0.002 TRP B 180 HIS 0.002 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 3775) covalent geometry : angle 0.59664 / 0.29 ( 5121) SS BOND : bond 0.00242 / 0.12 ( 7) SS BOND : angle 0.83401 / 0.59 ( 14) hydrogen bonds : bond 0.02434 / 1.53 ( 137) hydrogen bonds : angle 5.25522 / 3.45 ( 369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 889.15 seconds wall clock time: 15 minutes 55.25 seconds (955.25 seconds total)