Starting phenix.real_space_refine on Tue Feb 3 12:47:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tbe_55766/02_2026/9tbe_55766.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tbe_55766/02_2026/9tbe_55766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tbe_55766/02_2026/9tbe_55766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tbe_55766/02_2026/9tbe_55766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tbe_55766/02_2026/9tbe_55766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tbe_55766/02_2026/9tbe_55766.map" } resolution = 2.8 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 10 5.16 5 C 1610 2.51 5 N 349 2.21 5 O 411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2380 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2162 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "D" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 218 Unusual residues: {'LFA': 11, 'LMT': 2, 'RET': 1} Classifications: {'undetermined': 14, 'water': 20} Link IDs: {None: 33} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 0.68, per 1000 atoms: 0.29 Number of scatterers: 2380 At special positions: 0 Unit cell: (46.464, 55.176, 84.216, 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 10 16.00 O 411 8.00 N 349 7.00 C 1610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 77.2 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 80.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 11 through 39 removed outlier: 3.619A pdb=" N ILE D 18 " --> pdb=" O GLN D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 75 removed outlier: 3.709A pdb=" N ALA D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 117 removed outlier: 4.071A pdb=" N TYR D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Proline residue: D 107 - end of helix removed outlier: 3.522A pdb=" N LEU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 146 removed outlier: 3.619A pdb=" N MET D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 Processing helix chain 'D' and resid 168 through 187 removed outlier: 3.589A pdb=" N ALA D 173 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 213 removed outlier: 3.573A pdb=" N SER D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 220 removed outlier: 3.846A pdb=" N PHE D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 227 through 265 removed outlier: 3.577A pdb=" N ALA D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 Processing sheet with id=AA1, first strand: chain 'D' and resid 76 through 79 152 hydrogen bonds defined for protein. 447 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: 0.31 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 330 1.31 - 1.44: 722 1.44 - 1.57: 1348 1.57 - 1.69: 0 1.69 - 1.82: 18 Bond restraints: 2418 Sorted by residual: bond pdb=" C GLU D 267 " pdb=" N PRO D 268 " ideal model delta sigma weight residual 1.335 1.389 -0.054 1.28e-02 6.10e+03 1.79e+01 bond pdb=" C LYS D 246A" pdb=" O LYS D 246A" ideal model delta sigma weight residual 1.235 1.186 0.049 1.26e-02 6.30e+03 1.52e+01 bond pdb=" C GLU D 149 " pdb=" N PRO D 150 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.28e-02 6.10e+03 1.48e+01 bond pdb=" C8 RET D 514 " pdb=" C9 RET D 514 " ideal model delta sigma weight residual 1.450 1.386 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C14 RET D 514 " pdb=" C15 RET D 514 " ideal model delta sigma weight residual 1.448 1.507 -0.059 2.00e-02 2.50e+03 8.58e+00 ... (remaining 2413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 3018 1.70 - 3.40: 187 3.40 - 5.10: 33 5.10 - 6.79: 12 6.79 - 8.49: 4 Bond angle restraints: 3254 Sorted by residual: angle pdb=" N ILE D 104 " pdb=" CA ILE D 104 " pdb=" C ILE D 104 " ideal model delta sigma weight residual 111.81 108.25 3.56 8.60e-01 1.35e+00 1.72e+01 angle pdb=" N VAL D 136 " pdb=" CA VAL D 136 " pdb=" C VAL D 136 " ideal model delta sigma weight residual 111.58 107.25 4.33 1.06e+00 8.90e-01 1.67e+01 angle pdb=" O SER D 245 " pdb=" C SER D 245 " pdb=" N LYS D 246A" ideal model delta sigma weight residual 122.39 117.78 4.61 1.29e+00 6.01e-01 1.28e+01 angle pdb=" C LYS D 246A" pdb=" CA LYS D 246A" pdb=" CB LYS D 246A" ideal model delta sigma weight residual 110.42 117.51 -7.09 1.99e+00 2.53e-01 1.27e+01 angle pdb=" N LYS D 246A" pdb=" CA LYS D 246A" pdb=" CB LYS D 246A" ideal model delta sigma weight residual 110.49 104.62 5.87 1.69e+00 3.50e-01 1.21e+01 ... (remaining 3249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 1312 21.84 - 43.69: 118 43.69 - 65.53: 34 65.53 - 87.37: 4 87.37 - 109.22: 3 Dihedral angle restraints: 1471 sinusoidal: 680 harmonic: 791 Sorted by residual: dihedral pdb=" C1 RET D 514 " pdb=" C2 RET D 514 " pdb=" C3 RET D 514 " pdb=" C4 RET D 514 " ideal model delta sinusoidal sigma weight residual -62.54 46.68 -109.22 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C2 RET D 514 " pdb=" C3 RET D 514 " pdb=" C4 RET D 514 " pdb=" C5 RET D 514 " ideal model delta sinusoidal sigma weight residual 42.40 -58.87 101.27 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" CA ASN D 184 " pdb=" C ASN D 184 " pdb=" N ALA D 185 " pdb=" CA ALA D 185 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 1468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 227 0.043 - 0.085: 102 0.085 - 0.128: 23 0.128 - 0.170: 4 0.170 - 0.213: 1 Chirality restraints: 357 Sorted by residual: chirality pdb=" CA GLU D 149 " pdb=" N GLU D 149 " pdb=" C GLU D 149 " pdb=" CB GLU D 149 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ASN D 184 " pdb=" N ASN D 184 " pdb=" C ASN D 184 " pdb=" CB ASN D 184 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA TYR D 215 " pdb=" N TYR D 215 " pdb=" C TYR D 215 " pdb=" CB TYR D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 354 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET D 514 " -0.107 2.00e-02 2.50e+03 3.21e-01 1.29e+03 pdb=" C13 RET D 514 " 0.116 2.00e-02 2.50e+03 pdb=" C14 RET D 514 " 0.557 2.00e-02 2.50e+03 pdb=" C15 RET D 514 " -0.379 2.00e-02 2.50e+03 pdb=" C20 RET D 514 " -0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 RET D 514 " -0.094 2.00e-02 2.50e+03 9.20e-02 8.46e+01 pdb=" C11 RET D 514 " 0.099 2.00e-02 2.50e+03 pdb=" C12 RET D 514 " 0.085 2.00e-02 2.50e+03 pdb=" C13 RET D 514 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 245 " -0.021 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C SER D 245 " 0.070 2.00e-02 2.50e+03 pdb=" O SER D 245 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS D 246A" -0.024 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 1168 3.04 - 3.50: 2430 3.50 - 3.97: 3994 3.97 - 4.43: 4823 4.43 - 4.90: 7638 Nonbonded interactions: 20053 Sorted by model distance: nonbonded pdb=" O SER D 245 " pdb=" CA LYS D 246A" model vdw 2.571 2.776 nonbonded pdb=" N LEU D 223 " pdb=" N PHE D 224 " model vdw 2.611 2.560 nonbonded pdb=" N ILE D 4 " pdb=" N GLU D 5 " model vdw 2.612 2.560 nonbonded pdb=" N THR D 227 " pdb=" O THR D 227 " model vdw 2.621 2.496 nonbonded pdb=" O LYS D 246A" pdb=" CA LEU D 247 " model vdw 2.643 2.776 ... (remaining 20048 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.290 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.005 0.064 2419 Z= 0.292 Angle : 1.001 8.493 3254 Z= 0.580 Chirality : 0.049 0.213 357 Planarity : 0.019 0.321 384 Dihedral : 17.995 109.217 963 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.17 % Allowed : 21.72 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.45), residues: 270 helix: -1.01 (0.32), residues: 208 sheet: None (None), residues: 0 loop : -1.73 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 187 TYR 0.012 0.001 TYR D 215 PHE 0.011 0.002 PHE D 164 TRP 0.016 0.002 TRP D 69 HIS 0.001 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 2418) covalent geometry : angle 1.00058 ( 3254) hydrogen bonds : bond 0.19527 ( 152) hydrogen bonds : angle 6.73070 ( 447) Misc. bond : bond 0.02107 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.048 Fit side-chains REVERT: D 46 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.7854 (p0) REVERT: D 74 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7129 (tp30) REVERT: D 140 LEU cc_start: 0.7377 (mt) cc_final: 0.6722 (pp) REVERT: D 190 GLN cc_start: 0.7149 (mm-40) cc_final: 0.6816 (mt0) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.2806 time to fit residues: 11.8489 Evaluate side-chains 39 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147580 restraints weight = 2953.148| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.11 r_work: 0.3623 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2419 Z= 0.122 Angle : 0.577 6.861 3254 Z= 0.285 Chirality : 0.037 0.131 357 Planarity : 0.006 0.040 384 Dihedral : 10.018 56.205 517 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.43 % Allowed : 17.19 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.51), residues: 270 helix: 0.22 (0.35), residues: 214 sheet: None (None), residues: 0 loop : -0.45 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 127 TYR 0.010 0.001 TYR D 215 PHE 0.009 0.001 PHE D 12 TRP 0.015 0.001 TRP D 165 HIS 0.003 0.002 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2418) covalent geometry : angle 0.57704 ( 3254) hydrogen bonds : bond 0.04362 ( 152) hydrogen bonds : angle 4.04123 ( 447) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.050 Fit side-chains revert: symmetry clash REVERT: D 74 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7354 (tp30) REVERT: D 125 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5571 (tmm160) REVERT: D 140 LEU cc_start: 0.7801 (mt) cc_final: 0.7564 (mm) REVERT: D 190 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7109 (mt0) outliers start: 12 outliers final: 4 residues processed: 40 average time/residue: 0.3118 time to fit residues: 12.8155 Evaluate side-chains 34 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 238 TYR Chi-restraints excluded: chain D residue 246 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.0070 chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.157230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146433 restraints weight = 2990.723| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.13 r_work: 0.3595 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2419 Z= 0.117 Angle : 0.550 6.717 3254 Z= 0.270 Chirality : 0.037 0.125 357 Planarity : 0.005 0.036 384 Dihedral : 9.023 54.380 510 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.88 % Allowed : 17.19 % Favored : 76.92 % 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 are not related in a simple way. whole: 0.65 (0.52), residues: 270 helix: 0.67 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -0.04 (0.88), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 98 TYR 0.009 0.001 TYR D 215 PHE 0.007 0.001 PHE D 12 TRP 0.016 0.001 TRP D 165 HIS 0.003 0.002 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2418) covalent geometry : angle 0.55003 ( 3254) hydrogen bonds : bond 0.04125 ( 152) hydrogen bonds : angle 3.81204 ( 447) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.049 Fit side-chains revert: symmetry clash REVERT: D 74 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7377 (tp30) REVERT: D 125 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5652 (tmm160) REVERT: D 140 LEU cc_start: 0.7844 (mt) cc_final: 0.7620 (mm) REVERT: D 190 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7086 (mt0) outliers start: 13 outliers final: 4 residues processed: 41 average time/residue: 0.3425 time to fit residues: 14.3936 Evaluate side-chains 33 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 246 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 184 ASN D 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.154377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143057 restraints weight = 2967.971| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.20 r_work: 0.3554 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2419 Z= 0.154 Angle : 0.592 6.841 3254 Z= 0.290 Chirality : 0.039 0.140 357 Planarity : 0.005 0.036 384 Dihedral : 9.254 54.300 508 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.52 % Allowed : 19.00 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.53), residues: 270 helix: 0.67 (0.36), residues: 212 sheet: None (None), residues: 0 loop : 0.13 (0.91), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 234 TYR 0.010 0.001 TYR D 143 PHE 0.010 0.001 PHE D 12 TRP 0.021 0.002 TRP D 165 HIS 0.003 0.002 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 2418) covalent geometry : angle 0.59178 ( 3254) hydrogen bonds : bond 0.04556 ( 152) hydrogen bonds : angle 3.89032 ( 447) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.050 Fit side-chains revert: symmetry clash REVERT: D 74 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7388 (tp30) REVERT: D 125 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5736 (tmm160) REVERT: D 140 LEU cc_start: 0.7841 (mt) cc_final: 0.7618 (mm) REVERT: D 190 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7126 (mt0) REVERT: D 235 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7802 (mp-120) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.3006 time to fit residues: 12.3601 Evaluate side-chains 37 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 246 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 184 ASN D 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142221 restraints weight = 2969.593| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.20 r_work: 0.3586 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2419 Z= 0.157 Angle : 0.587 6.851 3254 Z= 0.289 Chirality : 0.039 0.134 357 Planarity : 0.004 0.036 384 Dihedral : 9.098 54.579 506 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.88 % Allowed : 18.10 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.52), residues: 270 helix: 0.67 (0.36), residues: 212 sheet: None (None), residues: 0 loop : 0.14 (0.91), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 127 TYR 0.010 0.001 TYR D 143 PHE 0.009 0.001 PHE D 12 TRP 0.020 0.002 TRP D 165 HIS 0.003 0.002 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2418) covalent geometry : angle 0.58710 ( 3254) hydrogen bonds : bond 0.04542 ( 152) hydrogen bonds : angle 3.90278 ( 447) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: D 74 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7208 (tp30) REVERT: D 108 MET cc_start: 0.7482 (mmp) cc_final: 0.7184 (mmp) REVERT: D 125 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.5727 (tmm160) REVERT: D 140 LEU cc_start: 0.7795 (mt) cc_final: 0.7588 (mm) REVERT: D 190 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7131 (mt0) REVERT: D 235 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7634 (mp-120) outliers start: 13 outliers final: 7 residues processed: 43 average time/residue: 0.3972 time to fit residues: 17.4949 Evaluate side-chains 38 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 TYR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 246 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 184 ASN D 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143858 restraints weight = 2929.724| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.18 r_work: 0.3612 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2419 Z= 0.132 Angle : 0.569 7.130 3254 Z= 0.280 Chirality : 0.039 0.136 357 Planarity : 0.005 0.035 384 Dihedral : 8.840 54.380 506 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.52 % Allowed : 19.91 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.52), residues: 270 helix: 0.77 (0.36), residues: 212 sheet: None (None), residues: 0 loop : 0.25 (0.91), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 234 TYR 0.010 0.001 TYR D 143 PHE 0.007 0.001 PHE D 12 TRP 0.017 0.001 TRP D 165 HIS 0.002 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 2418) covalent geometry : angle 0.56911 ( 3254) hydrogen bonds : bond 0.04296 ( 152) hydrogen bonds : angle 3.81815 ( 447) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.049 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8075 (p0) REVERT: D 74 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7211 (tp30) REVERT: D 108 MET cc_start: 0.7466 (mmp) cc_final: 0.7183 (mmp) REVERT: D 125 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.5735 (tmm160) REVERT: D 140 LEU cc_start: 0.7758 (mt) cc_final: 0.7556 (mm) REVERT: D 190 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7206 (mt0) REVERT: D 235 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7543 (mp-120) outliers start: 10 outliers final: 6 residues processed: 39 average time/residue: 0.2934 time to fit residues: 11.7881 Evaluate side-chains 38 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 TYR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 246 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.156164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145875 restraints weight = 2953.583| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.03 r_work: 0.3610 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2419 Z= 0.135 Angle : 0.575 7.348 3254 Z= 0.282 Chirality : 0.039 0.134 357 Planarity : 0.004 0.034 384 Dihedral : 8.741 54.329 506 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.07 % Allowed : 20.81 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.52), residues: 270 helix: 0.77 (0.36), residues: 210 sheet: None (None), residues: 0 loop : 0.35 (0.89), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 98 TYR 0.010 0.001 TYR D 143 PHE 0.007 0.001 PHE D 12 TRP 0.017 0.001 TRP D 165 HIS 0.002 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2418) covalent geometry : angle 0.57545 ( 3254) hydrogen bonds : bond 0.04299 ( 152) hydrogen bonds : angle 3.79826 ( 447) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.050 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.7912 (p0) REVERT: D 74 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7009 (tp30) REVERT: D 108 MET cc_start: 0.7216 (mmp) cc_final: 0.6935 (mmp) REVERT: D 124 LEU cc_start: 0.7638 (tp) cc_final: 0.7389 (tp) REVERT: D 125 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5559 (tmm160) REVERT: D 190 GLN cc_start: 0.7648 (mm-40) cc_final: 0.6999 (mt0) REVERT: D 235 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7253 (mp-120) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 0.4114 time to fit residues: 16.4632 Evaluate side-chains 39 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 TYR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 246 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.0040 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145226 restraints weight = 2902.453| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.04 r_work: 0.3641 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2419 Z= 0.131 Angle : 0.571 7.502 3254 Z= 0.280 Chirality : 0.039 0.139 357 Planarity : 0.004 0.034 384 Dihedral : 8.634 54.221 506 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.98 % Allowed : 19.46 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.52), residues: 270 helix: 0.84 (0.36), residues: 210 sheet: None (None), residues: 0 loop : 0.40 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 98 TYR 0.010 0.001 TYR D 143 PHE 0.007 0.001 PHE D 12 TRP 0.016 0.001 TRP D 165 HIS 0.002 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2418) covalent geometry : angle 0.57139 ( 3254) hydrogen bonds : bond 0.04245 ( 152) hydrogen bonds : angle 3.77900 ( 447) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.7996 (p0) REVERT: D 74 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7104 (tp30) REVERT: D 108 MET cc_start: 0.7311 (mmp) cc_final: 0.7045 (mmp) REVERT: D 124 LEU cc_start: 0.7747 (tp) cc_final: 0.7527 (tp) REVERT: D 125 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5617 (tmm160) REVERT: D 190 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7094 (mt0) REVERT: D 235 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7332 (mp-120) outliers start: 11 outliers final: 7 residues processed: 41 average time/residue: 0.3402 time to fit residues: 14.3579 Evaluate side-chains 39 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 TYR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 246 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.155068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144838 restraints weight = 2989.014| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.03 r_work: 0.3631 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2419 Z= 0.140 Angle : 0.582 7.594 3254 Z= 0.286 Chirality : 0.040 0.144 357 Planarity : 0.004 0.034 384 Dihedral : 8.689 54.373 506 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.52 % Allowed : 19.46 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.51), residues: 270 helix: 0.72 (0.36), residues: 213 sheet: None (None), residues: 0 loop : 0.10 (0.83), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 234 TYR 0.010 0.001 TYR D 143 PHE 0.008 0.001 PHE D 12 TRP 0.017 0.001 TRP D 165 HIS 0.002 0.002 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2418) covalent geometry : angle 0.58169 ( 3254) hydrogen bonds : bond 0.04349 ( 152) hydrogen bonds : angle 3.80724 ( 447) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8008 (p0) REVERT: D 74 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7115 (tp30) REVERT: D 108 MET cc_start: 0.7311 (mmp) cc_final: 0.7051 (mmp) REVERT: D 124 LEU cc_start: 0.7783 (tp) cc_final: 0.7556 (tp) REVERT: D 125 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5637 (tmm160) REVERT: D 190 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7117 (mt0) outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.4389 time to fit residues: 17.1032 Evaluate side-chains 39 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 TYR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 246 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 12 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: D 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.154332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143921 restraints weight = 3001.839| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.06 r_work: 0.3587 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2419 Z= 0.147 Angle : 0.589 7.589 3254 Z= 0.290 Chirality : 0.040 0.146 357 Planarity : 0.004 0.034 384 Dihedral : 8.760 54.482 506 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.52 % Allowed : 19.46 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.51), residues: 270 helix: 0.70 (0.36), residues: 213 sheet: None (None), residues: 0 loop : 0.12 (0.83), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 187 TYR 0.010 0.001 TYR D 143 PHE 0.008 0.001 PHE D 12 TRP 0.018 0.001 TRP D 165 HIS 0.003 0.002 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 2418) covalent geometry : angle 0.58873 ( 3254) hydrogen bonds : bond 0.04425 ( 152) hydrogen bonds : angle 3.83200 ( 447) Misc. bond : bond 0.00050 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.7948 (p0) REVERT: D 74 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7032 (tp30) REVERT: D 108 MET cc_start: 0.7223 (mmp) cc_final: 0.6962 (mmp) REVERT: D 124 LEU cc_start: 0.7729 (tp) cc_final: 0.7517 (tp) REVERT: D 125 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5567 (tmm160) REVERT: D 190 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7052 (mt0) outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.5236 time to fit residues: 20.4197 Evaluate side-chains 39 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 TYR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 246 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.156009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145785 restraints weight = 2936.652| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.03 r_work: 0.3635 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2419 Z= 0.124 Angle : 0.569 7.583 3254 Z= 0.280 Chirality : 0.039 0.144 357 Planarity : 0.004 0.033 384 Dihedral : 8.523 54.291 506 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.52 % Allowed : 19.91 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.51), residues: 270 helix: 0.81 (0.36), residues: 213 sheet: None (None), residues: 0 loop : 0.18 (0.83), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 98 TYR 0.009 0.001 TYR D 143 PHE 0.007 0.001 PHE D 12 TRP 0.015 0.001 TRP D 165 HIS 0.002 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2418) covalent geometry : angle 0.56922 ( 3254) hydrogen bonds : bond 0.04178 ( 152) hydrogen bonds : angle 3.75678 ( 447) Misc. bond : bond 0.00068 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 880.29 seconds wall clock time: 15 minutes 47.03 seconds (947.03 seconds total)