Starting phenix.real_space_refine on Tue Aug 4 11:47:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z3y_73795/08_2026/9z3y_73795.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z3y_73795/08_2026/9z3y_73795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z3y_73795/08_2026/9z3y_73795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z3y_73795/08_2026/9z3y_73795.map" model { file = "/net/cci-nas-00/data/ceres_data/9z3y_73795/08_2026/9z3y_73795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z3y_73795/08_2026/9z3y_73795.cif" } resolution = 2.99 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= 0.011 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 4 5.16 5 C 1256 2.51 5 N 309 2.21 5 O 367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1936 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1838 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 0.87, per 1000 atoms: 0.45 Number of scatterers: 1936 At special positions: 0 Unit cell: (57.408, 54.08, 65.728, 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 4 16.00 O 367 8.00 N 309 7.00 C 1256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 154 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 221 " " NAG B1301 " - " ASN B 269 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 153 " " NAG B1305 " - " ASN B 99 " Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 68.7 milliseconds 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 424 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 30 removed outlier: 5.959A pdb=" N PHE B 189 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP B 215 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 191 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.788A pdb=" N GLY B 103 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 156 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU B 132 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS B 154 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLN B 134 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N LYS B 152 " --> pdb=" O GLN B 134 " (cutoff:3.500A) 69 hydrogen bonds defined for protein. 180 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: 0.27 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 577 1.34 - 1.46: 537 1.46 - 1.58: 868 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 1988 Sorted by residual: bond pdb=" N SER B 145 " pdb=" CA SER B 145 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.24e-02 6.50e+03 4.20e+00 bond pdb=" N GLU B 142 " pdb=" CA GLU B 142 " ideal model delta sigma weight residual 1.464 1.487 -0.023 1.20e-02 6.94e+03 3.82e+00 bond pdb=" N GLU B 144 " pdb=" CA GLU B 144 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.51e-02 4.39e+03 3.47e+00 bond pdb=" N SER B 143 " pdb=" CA SER B 143 " ideal model delta sigma weight residual 1.461 1.487 -0.026 1.52e-02 4.33e+03 2.99e+00 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.446 -0.033 2.00e-02 2.50e+03 2.65e+00 ... (remaining 1983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2518 1.12 - 2.25: 128 2.25 - 3.37: 39 3.37 - 4.49: 10 4.49 - 5.62: 2 Bond angle restraints: 2697 Sorted by residual: angle pdb=" N ILE B 199 " pdb=" CA ILE B 199 " pdb=" C ILE B 199 " ideal model delta sigma weight residual 113.71 110.02 3.69 9.50e-01 1.11e+00 1.51e+01 angle pdb=" CA GLU B 144 " pdb=" C GLU B 144 " pdb=" O GLU B 144 " ideal model delta sigma weight residual 121.84 117.44 4.40 1.16e+00 7.43e-01 1.44e+01 angle pdb=" N VAL B 147 " pdb=" CA VAL B 147 " pdb=" C VAL B 147 " ideal model delta sigma weight residual 111.62 108.77 2.85 7.90e-01 1.60e+00 1.30e+01 angle pdb=" CA SER B 143 " pdb=" C SER B 143 " pdb=" O SER B 143 " ideal model delta sigma weight residual 121.54 118.01 3.53 1.16e+00 7.43e-01 9.25e+00 angle pdb=" CA SER B 145 " pdb=" C SER B 145 " pdb=" O SER B 145 " ideal model delta sigma weight residual 122.38 118.08 4.30 1.49e+00 4.50e-01 8.34e+00 ... (remaining 2692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 1124 21.76 - 43.51: 89 43.51 - 65.27: 21 65.27 - 87.02: 7 87.02 - 108.78: 4 Dihedral angle restraints: 1245 sinusoidal: 587 harmonic: 658 Sorted by residual: dihedral pdb=" C3 NAG B1305 " pdb=" C4 NAG B1305 " pdb=" C5 NAG B1305 " pdb=" C6 NAG B1305 " ideal model delta sinusoidal sigma weight residual -179.69 -70.91 -108.78 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C3 NAG B1305 " pdb=" C4 NAG B1305 " pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sinusoidal sigma weight residual -58.04 50.57 -108.61 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C6 NAG B1305 " pdb=" C4 NAG B1305 " pdb=" C5 NAG B1305 " pdb=" O4 NAG B1305 " ideal model delta sinusoidal sigma weight residual -61.70 -166.63 104.93 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 1242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 262 0.055 - 0.111: 37 0.111 - 0.166: 12 0.166 - 0.221: 1 0.221 - 0.277: 1 Chirality restraints: 313 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" C2 NAG A 1 " pdb=" C1 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" N2 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.35 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 310 not shown) Planarity restraints: 339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 111 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" CG ASP B 111 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP B 111 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 111 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 216 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO B 217 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.009 2.00e-02 2.50e+03 7.73e-03 7.47e-01 pdb=" C7 NAG B1305 " -0.002 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " -0.002 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.012 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " 0.008 2.00e-02 2.50e+03 ... (remaining 336 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 778 2.87 - 3.38: 1604 3.38 - 3.89: 2866 3.89 - 4.39: 3390 4.39 - 4.90: 5974 Nonbonded interactions: 14612 Sorted by model distance: nonbonded pdb=" O ASP B 80 " pdb=" OD1 ASN B 81 " model vdw 2.367 3.040 nonbonded pdb=" O GLU B 96 " pdb=" OE1 GLU B 96 " model vdw 2.470 3.040 nonbonded pdb=" OD1 ASP B 202 " pdb=" N LEU B 203 " model vdw 2.508 3.120 nonbonded pdb=" O ASN B 81 " pdb=" OD1 ASN B 81 " model vdw 2.509 3.040 nonbonded pdb=" N GLU B 96 " pdb=" OE1 GLU B 96 " model vdw 2.510 3.120 ... (remaining 14607 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: 7.910 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: 0.020 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.760 Find NCS groups from input model: 0.010 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:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 0.033 1996 Z= 0.186 Angle : 0.692 9.412 2720 Z= 0.376 Chirality : 0.049 0.277 313 Planarity : 0.003 0.025 333 Dihedral : 17.765 108.780 818 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.49 % Allowed : 24.51 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.61), residues: 219 helix: None (None), residues: 0 sheet: -0.43 (0.54), residues: 91 loop : -1.23 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 201 TYR 0.006 0.001 TYR B 252 PHE 0.004 0.001 PHE B 43 TRP 0.005 0.001 TRP B 140 HIS 0.001 0.000 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.19 ( 1988) covalent geometry : angle 0.64613 / 0.37 ( 2697) SS BOND : bond 0.00217 / 0.14 ( 1) SS BOND : angle 0.96703 / 0.52 ( 2) hydrogen bonds : bond 0.17015 / 11.52 ( 69) hydrogen bonds : angle 8.87835 / 5.99 ( 180) link_BETA1-4 : bond 0.00658 / 0.44 ( 1) link_BETA1-4 : angle 2.23916 / 1.64 ( 3) link_NAG-ASN : bond 0.00610 / 0.42 ( 6) link_NAG-ASN : angle 2.97609 / 1.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.083 Fit side-chains REVERT: B 79 PHE cc_start: 0.6150 (OUTLIER) cc_final: 0.5518 (t80) REVERT: B 115 GLN cc_start: 0.8477 (mt0) cc_final: 0.7911 (mm-40) REVERT: B 152 LYS cc_start: 0.8000 (mptt) cc_final: 0.7749 (mmtt) REVERT: B 265 LYS cc_start: 0.8777 (ttpp) cc_final: 0.6404 (pmtt) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.8198 time to fit residues: 24.1480 Evaluate side-chains 27 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.079297 restraints weight = 3043.101| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.66 r_work: 0.2865 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 1996 Z= 0.197 Angle : 0.694 9.414 2720 Z= 0.326 Chirality : 0.052 0.305 313 Planarity : 0.004 0.037 333 Dihedral : 8.944 55.200 393 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.41 % Allowed : 22.06 % Favored : 73.53 % 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: -1.32 (0.59), residues: 219 helix: None (None), residues: 0 sheet: -0.06 (0.56), residues: 81 loop : -1.44 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 201 TYR 0.010 0.001 TYR B 252 PHE 0.010 0.001 PHE B 86 TRP 0.004 0.001 TRP B 140 HIS 0.001 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 1988) covalent geometry : angle 0.65250 / 0.32 ( 2697) SS BOND : bond 0.00224 / 0.15 ( 1) SS BOND : angle 0.94971 / 0.63 ( 2) hydrogen bonds : bond 0.02971 / 1.94 ( 69) hydrogen bonds : angle 6.17108 / 4.08 ( 180) link_BETA1-4 : bond 0.00128 / 0.09 ( 1) link_BETA1-4 : angle 1.23093 / 0.86 ( 3) link_NAG-ASN : bond 0.00431 / 0.29 ( 6) link_NAG-ASN : angle 2.93787 / 1.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.080 Fit side-chains REVERT: B 78 ARG cc_start: 0.6341 (tmt90) cc_final: 0.6124 (tmt90) REVERT: B 79 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.5516 (t80) REVERT: B 115 GLN cc_start: 0.8474 (mt0) cc_final: 0.7606 (mm-40) REVERT: B 152 LYS cc_start: 0.7889 (mptt) cc_final: 0.7585 (mmtt) REVERT: B 265 LYS cc_start: 0.8898 (ttpp) cc_final: 0.6448 (pmtt) outliers start: 9 outliers final: 3 residues processed: 37 average time/residue: 0.7303 time to fit residues: 27.4335 Evaluate side-chains 32 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.113412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.080178 restraints weight = 3095.224| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.77 r_work: 0.2882 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1996 Z= 0.136 Angle : 0.639 9.493 2720 Z= 0.305 Chirality : 0.050 0.265 313 Planarity : 0.003 0.034 333 Dihedral : 7.882 56.745 393 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.39 % Allowed : 24.51 % Favored : 70.10 % 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: -1.14 (0.60), residues: 219 helix: None (None), residues: 0 sheet: 0.08 (0.57), residues: 81 loop : -1.34 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 201 TYR 0.008 0.001 TYR B 252 PHE 0.008 0.001 PHE B 43 TRP 0.005 0.001 TRP B 140 HIS 0.001 0.000 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 1988) covalent geometry : angle 0.59867 / 0.30 ( 2697) SS BOND : bond 0.00148 / 0.10 ( 1) SS BOND : angle 1.43341 / 0.94 ( 2) hydrogen bonds : bond 0.02725 / 1.76 ( 69) hydrogen bonds : angle 5.81856 / 3.83 ( 180) link_BETA1-4 : bond 0.00282 / 0.19 ( 1) link_BETA1-4 : angle 1.42827 / 1.08 ( 3) link_NAG-ASN : bond 0.00407 / 0.26 ( 6) link_NAG-ASN : angle 2.71579 / 1.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.080 Fit side-chains REVERT: B 79 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5529 (t80) REVERT: B 96 GLU cc_start: 0.7863 (pm20) cc_final: 0.7597 (pm20) REVERT: B 102 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7417 (mmp80) REVERT: B 115 GLN cc_start: 0.8440 (mt0) cc_final: 0.7607 (mm-40) REVERT: B 152 LYS cc_start: 0.7903 (mptt) cc_final: 0.7484 (mmtt) REVERT: B 194 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.7654 (ttmm) REVERT: B 224 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.6707 (ptm-80) REVERT: B 265 LYS cc_start: 0.8907 (ttpp) cc_final: 0.6460 (pmtt) outliers start: 11 outliers final: 4 residues processed: 40 average time/residue: 0.7592 time to fit residues: 30.8088 Evaluate side-chains 32 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 224 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.109977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.077807 restraints weight = 3043.799| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.50 r_work: 0.2840 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1996 Z= 0.223 Angle : 0.686 9.563 2720 Z= 0.330 Chirality : 0.050 0.239 313 Planarity : 0.004 0.037 333 Dihedral : 7.812 56.241 393 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.88 % Allowed : 25.49 % Favored : 68.63 % 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: -1.21 (0.60), residues: 219 helix: None (None), residues: 0 sheet: 0.10 (0.58), residues: 81 loop : -1.43 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 201 TYR 0.014 0.001 TYR B 252 PHE 0.012 0.001 PHE B 86 TRP 0.009 0.001 TRP B 140 HIS 0.001 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 ( 1988) covalent geometry : angle 0.64656 / 0.32 ( 2697) SS BOND : bond 0.00125 / 0.08 ( 1) SS BOND : angle 1.35724 / 0.90 ( 2) hydrogen bonds : bond 0.02973 / 1.90 ( 69) hydrogen bonds : angle 5.70728 / 3.74 ( 180) link_BETA1-4 : bond 0.00226 / 0.15 ( 1) link_BETA1-4 : angle 1.32892 / 0.95 ( 3) link_NAG-ASN : bond 0.00379 / 0.25 ( 6) link_NAG-ASN : angle 2.80674 / 1.41 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.080 Fit side-chains REVERT: B 96 GLU cc_start: 0.8012 (pm20) cc_final: 0.7666 (pm20) REVERT: B 115 GLN cc_start: 0.8484 (mt0) cc_final: 0.7714 (mm-40) REVERT: B 152 LYS cc_start: 0.7984 (mptt) cc_final: 0.7623 (mmtt) REVERT: B 224 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6829 (ptm-80) REVERT: B 265 LYS cc_start: 0.8884 (ttpp) cc_final: 0.6421 (pmtt) outliers start: 12 outliers final: 4 residues processed: 39 average time/residue: 0.7450 time to fit residues: 29.4802 Evaluate side-chains 31 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 224 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.111991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.079484 restraints weight = 2987.283| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.59 r_work: 0.2870 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1996 Z= 0.141 Angle : 0.647 9.552 2720 Z= 0.310 Chirality : 0.049 0.209 313 Planarity : 0.003 0.035 333 Dihedral : 7.182 56.570 391 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.39 % Allowed : 26.96 % Favored : 67.65 % 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: -1.10 (0.61), residues: 219 helix: None (None), residues: 0 sheet: 0.18 (0.59), residues: 81 loop : -1.36 (0.59), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 201 TYR 0.009 0.001 TYR B 252 PHE 0.008 0.001 PHE B 43 TRP 0.007 0.001 TRP B 140 HIS 0.001 0.000 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 1988) covalent geometry : angle 0.60702 / 0.30 ( 2697) SS BOND : bond 0.00286 / 0.19 ( 1) SS BOND : angle 1.70679 / 1.15 ( 2) hydrogen bonds : bond 0.02671 / 1.71 ( 69) hydrogen bonds : angle 5.49032 / 3.59 ( 180) link_BETA1-4 : bond 0.00241 / 0.16 ( 1) link_BETA1-4 : angle 1.54895 / 1.19 ( 3) link_NAG-ASN : bond 0.00416 / 0.27 ( 6) link_NAG-ASN : angle 2.70250 / 1.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.090 Fit side-chains REVERT: B 96 GLU cc_start: 0.7896 (pm20) cc_final: 0.7508 (pm20) REVERT: B 115 GLN cc_start: 0.8401 (mt0) cc_final: 0.7547 (mm-40) REVERT: B 152 LYS cc_start: 0.7999 (mptt) cc_final: 0.7590 (mmtt) REVERT: B 194 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.7707 (ttmm) REVERT: B 224 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.6930 (ptm-80) REVERT: B 265 LYS cc_start: 0.8886 (ttpp) cc_final: 0.6449 (pmtt) outliers start: 11 outliers final: 5 residues processed: 38 average time/residue: 0.7213 time to fit residues: 27.8226 Evaluate side-chains 32 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 224 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.111675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.079258 restraints weight = 2997.306| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.60 r_work: 0.2864 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1996 Z= 0.145 Angle : 0.651 9.497 2720 Z= 0.312 Chirality : 0.049 0.203 313 Planarity : 0.004 0.039 333 Dihedral : 7.118 56.529 391 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.94 % Allowed : 29.41 % Favored : 67.65 % 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: -1.08 (0.60), residues: 219 helix: None (None), residues: 0 sheet: 0.22 (0.58), residues: 81 loop : -1.36 (0.59), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 201 TYR 0.009 0.001 TYR B 252 PHE 0.008 0.001 PHE B 43 TRP 0.007 0.001 TRP B 140 HIS 0.001 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 1988) covalent geometry : angle 0.61084 / 0.30 ( 2697) SS BOND : bond 0.00445 / 0.30 ( 1) SS BOND : angle 2.18211 / 1.40 ( 2) hydrogen bonds : bond 0.02678 / 1.70 ( 69) hydrogen bonds : angle 5.40958 / 3.54 ( 180) link_BETA1-4 : bond 0.00275 / 0.18 ( 1) link_BETA1-4 : angle 1.45459 / 1.08 ( 3) link_NAG-ASN : bond 0.00406 / 0.26 ( 6) link_NAG-ASN : angle 2.67614 / 1.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.079 Fit side-chains REVERT: B 96 GLU cc_start: 0.7872 (pm20) cc_final: 0.7448 (pm20) REVERT: B 102 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7361 (mmt-90) REVERT: B 115 GLN cc_start: 0.8353 (mt0) cc_final: 0.7440 (mm-40) REVERT: B 152 LYS cc_start: 0.7968 (mptt) cc_final: 0.7549 (mmtt) REVERT: B 224 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.6892 (ptm-80) REVERT: B 265 LYS cc_start: 0.8895 (ttpp) cc_final: 0.6493 (pmtt) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.7753 time to fit residues: 25.1729 Evaluate side-chains 31 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 224 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.079218 restraints weight = 2976.744| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.58 r_work: 0.2874 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1996 Z= 0.154 Angle : 0.661 9.482 2720 Z= 0.317 Chirality : 0.049 0.199 313 Planarity : 0.003 0.039 333 Dihedral : 7.111 56.444 391 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.90 % Allowed : 27.45 % Favored : 67.65 % 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: -1.17 (0.60), residues: 219 helix: None (None), residues: 0 sheet: -0.19 (0.57), residues: 87 loop : -1.20 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 201 TYR 0.009 0.001 TYR B 252 PHE 0.008 0.001 PHE B 43 TRP 0.007 0.001 TRP B 140 HIS 0.001 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 1988) covalent geometry : angle 0.62144 / 0.31 ( 2697) SS BOND : bond 0.00367 / 0.24 ( 1) SS BOND : angle 2.65213 / 1.69 ( 2) hydrogen bonds : bond 0.02683 / 1.70 ( 69) hydrogen bonds : angle 5.39324 / 3.52 ( 180) link_BETA1-4 : bond 0.00264 / 0.18 ( 1) link_BETA1-4 : angle 1.45446 / 1.07 ( 3) link_NAG-ASN : bond 0.00405 / 0.26 ( 6) link_NAG-ASN : angle 2.65679 / 1.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.078 Fit side-chains REVERT: B 96 GLU cc_start: 0.7889 (pm20) cc_final: 0.7447 (pm20) REVERT: B 115 GLN cc_start: 0.8365 (mt0) cc_final: 0.7448 (mm-40) REVERT: B 152 LYS cc_start: 0.7974 (mptt) cc_final: 0.7555 (mmtt) REVERT: B 224 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8142 (mtm-85) REVERT: B 265 LYS cc_start: 0.8897 (ttpp) cc_final: 0.6500 (pmtt) outliers start: 10 outliers final: 6 residues processed: 36 average time/residue: 0.7151 time to fit residues: 26.1062 Evaluate side-chains 33 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 224 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 21 optimal weight: 0.0870 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.114611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.081448 restraints weight = 3025.842| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.66 r_work: 0.2893 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1996 Z= 0.122 Angle : 0.670 9.431 2720 Z= 0.324 Chirality : 0.049 0.202 313 Planarity : 0.004 0.042 333 Dihedral : 6.980 56.747 391 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.43 % Allowed : 28.92 % Favored : 67.65 % 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: -1.08 (0.61), residues: 219 helix: None (None), residues: 0 sheet: -0.13 (0.57), residues: 87 loop : -1.14 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 201 TYR 0.009 0.001 TYR B 252 PHE 0.008 0.001 PHE B 43 TRP 0.008 0.001 TRP B 140 HIS 0.000 0.000 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 1988) covalent geometry : angle 0.63228 / 0.31 ( 2697) SS BOND : bond 0.00749 / 0.50 ( 1) SS BOND : angle 3.07932 / 1.95 ( 2) hydrogen bonds : bond 0.02490 / 1.58 ( 69) hydrogen bonds : angle 5.28256 / 3.45 ( 180) link_BETA1-4 : bond 0.00292 / 0.19 ( 1) link_BETA1-4 : angle 1.50521 / 1.13 ( 3) link_NAG-ASN : bond 0.00414 / 0.27 ( 6) link_NAG-ASN : angle 2.56046 / 1.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.045 Fit side-chains REVERT: B 96 GLU cc_start: 0.7835 (pm20) cc_final: 0.7383 (pm20) REVERT: B 115 GLN cc_start: 0.8337 (mt0) cc_final: 0.7453 (mm-40) REVERT: B 152 LYS cc_start: 0.7937 (mptt) cc_final: 0.7522 (mmtt) REVERT: B 224 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8179 (mtm-85) REVERT: B 265 LYS cc_start: 0.8898 (ttpp) cc_final: 0.6518 (pmtt) outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.4744 time to fit residues: 15.9079 Evaluate side-chains 32 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 224 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.079695 restraints weight = 2957.889| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.62 r_work: 0.2868 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1996 Z= 0.165 Angle : 0.720 9.435 2720 Z= 0.350 Chirality : 0.050 0.203 313 Planarity : 0.004 0.049 333 Dihedral : 7.014 56.287 391 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.39 % Allowed : 27.45 % Favored : 67.16 % 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: -1.08 (0.60), residues: 219 helix: None (None), residues: 0 sheet: -0.09 (0.57), residues: 87 loop : -1.17 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 201 TYR 0.011 0.001 TYR B 252 PHE 0.008 0.001 PHE B 65 TRP 0.009 0.001 TRP B 140 HIS 0.001 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 1988) covalent geometry : angle 0.68188 / 0.34 ( 2697) SS BOND : bond 0.00207 / 0.14 ( 1) SS BOND : angle 3.69439 / 2.30 ( 2) hydrogen bonds : bond 0.02805 / 1.76 ( 69) hydrogen bonds : angle 5.30625 / 3.47 ( 180) link_BETA1-4 : bond 0.00304 / 0.20 ( 1) link_BETA1-4 : angle 1.38700 / 0.98 ( 3) link_NAG-ASN : bond 0.00382 / 0.25 ( 6) link_NAG-ASN : angle 2.59592 / 1.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: B 96 GLU cc_start: 0.7921 (pm20) cc_final: 0.7458 (pm20) REVERT: B 115 GLN cc_start: 0.8380 (mt0) cc_final: 0.7471 (mm-40) REVERT: B 152 LYS cc_start: 0.8071 (mptt) cc_final: 0.7703 (mmtt) REVERT: B 224 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8178 (mtm-85) REVERT: B 265 LYS cc_start: 0.8897 (ttpp) cc_final: 0.6532 (pmtt) outliers start: 11 outliers final: 7 residues processed: 35 average time/residue: 0.4648 time to fit residues: 16.5141 Evaluate side-chains 32 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 224 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.0270 chunk 14 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.080443 restraints weight = 3032.672| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.61 r_work: 0.2882 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1996 Z= 0.146 Angle : 0.737 9.430 2720 Z= 0.363 Chirality : 0.050 0.199 313 Planarity : 0.005 0.052 333 Dihedral : 7.017 56.572 391 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.90 % Allowed : 27.45 % Favored : 67.65 % 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: -1.05 (0.61), residues: 219 helix: None (None), residues: 0 sheet: 0.02 (0.58), residues: 85 loop : -1.21 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 201 TYR 0.009 0.001 TYR B 252 PHE 0.008 0.001 PHE B 65 TRP 0.008 0.001 TRP B 140 HIS 0.001 0.000 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 1988) covalent geometry : angle 0.69849 / 0.35 ( 2697) SS BOND : bond 0.00818 / 0.55 ( 1) SS BOND : angle 4.40847 / 2.76 ( 2) hydrogen bonds : bond 0.02667 / 1.67 ( 69) hydrogen bonds : angle 5.29538 / 3.47 ( 180) link_BETA1-4 : bond 0.00307 / 0.20 ( 1) link_BETA1-4 : angle 1.46139 / 1.08 ( 3) link_NAG-ASN : bond 0.00402 / 0.26 ( 6) link_NAG-ASN : angle 2.54015 / 1.27 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: B 96 GLU cc_start: 0.7796 (pm20) cc_final: 0.7326 (pm20) REVERT: B 115 GLN cc_start: 0.8374 (mt0) cc_final: 0.7453 (mm-40) REVERT: B 152 LYS cc_start: 0.7996 (mptt) cc_final: 0.7612 (mmtt) REVERT: B 224 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8141 (mtm-85) REVERT: B 265 LYS cc_start: 0.8885 (ttpp) cc_final: 0.6503 (pmtt) outliers start: 10 outliers final: 8 residues processed: 34 average time/residue: 0.4891 time to fit residues: 16.8673 Evaluate side-chains 34 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 224 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.080349 restraints weight = 3044.943| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.60 r_work: 0.2886 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 1996 Z= 0.282 Angle : 1.651 59.200 2720 Z= 0.997 Chirality : 0.065 0.731 313 Planarity : 0.006 0.063 333 Dihedral : 7.208 56.576 391 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.41 % Allowed : 27.94 % Favored : 67.65 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -1.07 (0.61), residues: 219 helix: None (None), residues: 0 sheet: 0.02 (0.58), residues: 85 loop : -1.24 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 201 TYR 0.009 0.001 TYR B 252 PHE 0.008 0.001 PHE B 65 TRP 0.008 0.001 TRP B 140 HIS 0.002 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.28 ( 1988) covalent geometry : angle 1.63553 / 1.00 ( 2697) SS BOND : bond 0.01412 / 0.94 ( 1) SS BOND : angle 6.12615 / 3.86 ( 2) hydrogen bonds : bond 0.02663 / 1.67 ( 69) hydrogen bonds : angle 5.29509 / 3.47 ( 180) link_BETA1-4 : bond 0.00347 / 0.23 ( 1) link_BETA1-4 : angle 1.46382 / 1.08 ( 3) link_NAG-ASN : bond 0.00403 / 0.26 ( 6) link_NAG-ASN : angle 2.54261 / 1.27 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 983.52 seconds wall clock time: 17 minutes 25.50 seconds (1045.50 seconds total)