Starting phenix.real_space_refine on Fri Aug 22 12:42:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bt9_44884/08_2025/9bt9_44884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bt9_44884/08_2025/9bt9_44884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bt9_44884/08_2025/9bt9_44884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bt9_44884/08_2025/9bt9_44884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bt9_44884/08_2025/9bt9_44884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bt9_44884/08_2025/9bt9_44884.map" } resolution = 2.11 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= -0.002 sd= 0.065 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 8 5.16 5 C 1526 2.51 5 N 356 2.21 5 O 475 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2365 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2192 Classifications: {'peptide': 268} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 258} Chain: "B" 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: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 Chain: "D" 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.91, per 1000 atoms: 0.38 Number of scatterers: 2365 At special positions: 0 Unit cell: (64.7215, 54.8335, 80.9018, 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 8 16.00 O 475 8.00 N 356 7.00 C 1526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1401 " - " ASN A 29 " " NAG A1402 " - " ASN A 58 " " NAG A1403 " - " ASN A 192 " " NAG A1404 " - " ASN A 251 " " NAG B 1 " - " ASN A 19 " " NAG C 1 " - " ASN A 132 " " NAG D 1 " - " ASN A 188 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 83.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 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: 1 helices and 6 sheets defined 1.5% alpha, 44.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.848A pdb=" N GLN A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 39 removed outlier: 3.962A pdb=" N ARG A 34 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE A 74 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 68 removed outlier: 3.605A pdb=" N ASN A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.993A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TRP A 174 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.528A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 113 69 hydrogen bonds defined for protein. 177 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: 0.35 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 620 1.33 - 1.45: 499 1.45 - 1.57: 1300 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 2429 Sorted by residual: bond pdb=" CZ ARG A 170 " pdb=" NH2 ARG A 170 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" C3 BMA C 3 " pdb=" O3 BMA C 3 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C5 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C5 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.413 1.483 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 2424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2095 1.44 - 2.87: 927 2.87 - 4.31: 252 4.31 - 5.74: 28 5.74 - 7.18: 9 Bond angle restraints: 3311 Sorted by residual: angle pdb=" N CYS A 151 " pdb=" CA CYS A 151 " pdb=" C CYS A 151 " ideal model delta sigma weight residual 111.71 118.69 -6.98 1.34e+00 5.57e-01 2.71e+01 angle pdb=" CA PHE A 121 " pdb=" CB PHE A 121 " pdb=" CG PHE A 121 " ideal model delta sigma weight residual 113.80 118.71 -4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" CB HIS A 234 " pdb=" CG HIS A 234 " pdb=" CD2 HIS A 234 " ideal model delta sigma weight residual 131.20 125.01 6.19 1.30e+00 5.92e-01 2.27e+01 angle pdb=" CB HIS A 175 " pdb=" CG HIS A 175 " pdb=" CD2 HIS A 175 " ideal model delta sigma weight residual 131.20 125.14 6.06 1.30e+00 5.92e-01 2.17e+01 angle pdb=" CB HIS A 201 " pdb=" CG HIS A 201 " pdb=" CD2 HIS A 201 " ideal model delta sigma weight residual 131.20 125.49 5.71 1.30e+00 5.92e-01 1.93e+01 ... (remaining 3306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.26: 1481 20.26 - 40.52: 67 40.52 - 60.78: 7 60.78 - 81.04: 6 81.04 - 101.30: 8 Dihedral angle restraints: 1569 sinusoidal: 770 harmonic: 799 Sorted by residual: dihedral pdb=" CA ALA A 150 " pdb=" C ALA A 150 " pdb=" N CYS A 151 " pdb=" CA CYS A 151 " ideal model delta harmonic sigma weight residual -180.00 -152.01 -27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA VAL A 113 " pdb=" C VAL A 113 " pdb=" N ASN A 114 " pdb=" CA ASN A 114 " ideal model delta harmonic sigma weight residual 180.00 -153.29 -26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA TYR A 266 " pdb=" C TYR A 266 " pdb=" N LEU A 267 " pdb=" CA LEU A 267 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 1566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 144 0.052 - 0.104: 109 0.104 - 0.156: 103 0.156 - 0.208: 40 0.208 - 0.259: 10 Chirality restraints: 406 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.92e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.41e+01 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.53 -0.13 2.00e-02 2.50e+03 3.93e+01 ... (remaining 403 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 256 " 0.116 2.00e-02 2.50e+03 7.16e-02 1.02e+02 pdb=" CG TYR A 256 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 256 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 256 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 256 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 256 " -0.061 2.00e-02 2.50e+03 pdb=" CZ TYR A 256 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 256 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 132 " -0.048 2.00e-02 2.50e+03 4.79e-02 2.86e+01 pdb=" CG ASN A 132 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 132 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 132 " 0.070 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 50 " 0.071 2.00e-02 2.50e+03 3.75e-02 2.82e+01 pdb=" CG TYR A 50 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 50 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 50 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 50 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 50 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 50 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 50 " 0.054 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 1396 3.05 - 3.51: 2140 3.51 - 3.97: 4151 3.97 - 4.44: 4576 4.44 - 4.90: 7431 Nonbonded interactions: 19694 Sorted by model distance: nonbonded pdb=" OD1 ASN A 108 " pdb=" OG SER A 119 " model vdw 2.582 3.040 nonbonded pdb=" OG SER A 36 " pdb=" O TYR A 38 " model vdw 2.585 3.040 nonbonded pdb=" OE2 GLU A 120 " pdb=" OG SER A 165 " model vdw 2.597 3.040 nonbonded pdb=" OD1 ASP A 17 " pdb=" O6 NAG C 1 " model vdw 2.604 3.040 nonbonded pdb=" OG1 THR A 154 " pdb=" OD1 ASP A 177 " model vdw 2.605 3.040 ... (remaining 19689 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } 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: 5.250 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: 0.000 Process input model: 4.910 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 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 : 0.015 0.073 2445 Z= 0.806 Angle : 1.719 8.527 3356 Z= 1.073 Chirality : 0.103 0.259 406 Planarity : 0.015 0.133 393 Dihedral : 14.403 101.301 1052 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.40 % Allowed : 0.00 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.45), residues: 266 helix: None (None), residues: 0 sheet: 0.17 (0.49), residues: 85 loop : -1.13 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG A 206 TYR 0.125 0.019 TYR A 256 PHE 0.041 0.011 PHE A 18 TRP 0.021 0.010 TRP A 89 HIS 0.009 0.005 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.01482 ( 2429) covalent geometry : angle 1.66289 ( 3311) SS BOND : bond 0.00429 ( 3) SS BOND : angle 1.40628 ( 6) hydrogen bonds : bond 0.09595 ( 69) hydrogen bonds : angle 7.89310 ( 177) link_ALPHA1-3 : bond 0.02740 ( 1) link_ALPHA1-3 : angle 5.14243 ( 3) link_ALPHA1-6 : bond 0.03112 ( 1) link_ALPHA1-6 : angle 4.32625 ( 3) link_BETA1-4 : bond 0.02177 ( 4) link_BETA1-4 : angle 4.09138 ( 12) link_NAG-ASN : bond 0.01098 ( 7) link_NAG-ASN : angle 4.45623 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.095 Fit side-chains REVERT: A 54 ARG cc_start: 0.9093 (mtt180) cc_final: 0.7395 (mmm160) REVERT: A 92 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8802 (mttp) REVERT: A 114 ASN cc_start: 0.8335 (m-40) cc_final: 0.8130 (m-40) REVERT: A 115 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8325 (mmtm) REVERT: A 155 MET cc_start: 0.9363 (mmm) cc_final: 0.8970 (mmm) REVERT: A 163 CYS cc_start: 0.8620 (m) cc_final: 0.8291 (m) REVERT: A 187 LYS cc_start: 0.9152 (tttt) cc_final: 0.8826 (tttp) REVERT: A 221 THR cc_start: 0.9204 (m) cc_final: 0.8981 (p) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.7836 time to fit residues: 34.2823 Evaluate side-chains 25 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3057 r_free = 0.3057 target = 0.082831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.068427 restraints weight = 3147.414| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.92 r_work: 0.2718 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2445 Z= 0.198 Angle : 0.708 4.738 3356 Z= 0.364 Chirality : 0.047 0.208 406 Planarity : 0.004 0.028 393 Dihedral : 10.745 79.697 566 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.62 % Allowed : 3.24 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.47), residues: 266 helix: None (None), residues: 0 sheet: 0.48 (0.51), residues: 90 loop : -0.90 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.018 0.002 TYR A 90 PHE 0.020 0.002 PHE A 18 TRP 0.020 0.002 TRP A 174 HIS 0.002 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 2429) covalent geometry : angle 0.67411 ( 3311) SS BOND : bond 0.00076 ( 3) SS BOND : angle 1.08953 ( 6) hydrogen bonds : bond 0.04904 ( 69) hydrogen bonds : angle 7.14618 ( 177) link_ALPHA1-3 : bond 0.00771 ( 1) link_ALPHA1-3 : angle 1.56857 ( 3) link_ALPHA1-6 : bond 0.00780 ( 1) link_ALPHA1-6 : angle 1.39025 ( 3) link_BETA1-4 : bond 0.00228 ( 4) link_BETA1-4 : angle 2.24697 ( 12) link_NAG-ASN : bond 0.00444 ( 7) link_NAG-ASN : angle 2.13080 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.111 Fit side-chains REVERT: A 54 ARG cc_start: 0.9235 (mtt180) cc_final: 0.7328 (mmm-85) REVERT: A 115 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8328 (mmtm) REVERT: A 247 SER cc_start: 0.8903 (p) cc_final: 0.8565 (m) outliers start: 4 outliers final: 0 residues processed: 30 average time/residue: 0.8595 time to fit residues: 26.2460 Evaluate side-chains 26 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3052 r_free = 0.3052 target = 0.082501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068443 restraints weight = 3180.921| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.89 r_work: 0.2728 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2445 Z= 0.173 Angle : 0.656 4.418 3356 Z= 0.339 Chirality : 0.045 0.217 406 Planarity : 0.004 0.031 393 Dihedral : 10.026 73.760 566 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.81 % Allowed : 5.26 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.49), residues: 266 helix: None (None), residues: 0 sheet: 0.42 (0.51), residues: 95 loop : -0.86 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.016 0.002 TYR A 66 PHE 0.018 0.002 PHE A 121 TRP 0.014 0.001 TRP A 174 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 2429) covalent geometry : angle 0.62621 ( 3311) SS BOND : bond 0.00261 ( 3) SS BOND : angle 1.61144 ( 6) hydrogen bonds : bond 0.04351 ( 69) hydrogen bonds : angle 6.98474 ( 177) link_ALPHA1-3 : bond 0.00798 ( 1) link_ALPHA1-3 : angle 1.23968 ( 3) link_ALPHA1-6 : bond 0.01150 ( 1) link_ALPHA1-6 : angle 1.17557 ( 3) link_BETA1-4 : bond 0.00189 ( 4) link_BETA1-4 : angle 1.94669 ( 12) link_NAG-ASN : bond 0.00426 ( 7) link_NAG-ASN : angle 1.91025 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.098 Fit side-chains REVERT: A 54 ARG cc_start: 0.9208 (mtt180) cc_final: 0.7314 (mmm-85) REVERT: A 115 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8369 (mmtm) REVERT: A 247 SER cc_start: 0.8882 (p) cc_final: 0.8579 (m) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.8496 time to fit residues: 22.4986 Evaluate side-chains 25 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.082169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.067938 restraints weight = 3183.519| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.90 r_work: 0.2721 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2445 Z= 0.208 Angle : 0.676 5.554 3356 Z= 0.347 Chirality : 0.046 0.235 406 Planarity : 0.004 0.035 393 Dihedral : 9.774 71.511 566 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.81 % Allowed : 6.88 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.50), residues: 266 helix: None (None), residues: 0 sheet: 0.30 (0.52), residues: 95 loop : -0.87 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.016 0.002 TYR A 66 PHE 0.017 0.002 PHE A 121 TRP 0.013 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 2429) covalent geometry : angle 0.64279 ( 3311) SS BOND : bond 0.00062 ( 3) SS BOND : angle 2.50276 ( 6) hydrogen bonds : bond 0.04256 ( 69) hydrogen bonds : angle 7.04416 ( 177) link_ALPHA1-3 : bond 0.00720 ( 1) link_ALPHA1-3 : angle 1.26448 ( 3) link_ALPHA1-6 : bond 0.01128 ( 1) link_ALPHA1-6 : angle 1.10727 ( 3) link_BETA1-4 : bond 0.00215 ( 4) link_BETA1-4 : angle 1.98917 ( 12) link_NAG-ASN : bond 0.00509 ( 7) link_NAG-ASN : angle 1.87512 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.091 Fit side-chains REVERT: A 54 ARG cc_start: 0.9235 (mtt180) cc_final: 0.7310 (mmm-85) REVERT: A 115 LYS cc_start: 0.8687 (mmmm) cc_final: 0.8294 (mmtm) REVERT: A 247 SER cc_start: 0.8908 (p) cc_final: 0.8592 (m) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.8554 time to fit residues: 21.7458 Evaluate side-chains 26 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.083259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.068911 restraints weight = 3146.227| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.91 r_work: 0.2733 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2445 Z= 0.177 Angle : 0.643 6.460 3356 Z= 0.331 Chirality : 0.045 0.239 406 Planarity : 0.004 0.038 393 Dihedral : 9.451 68.468 566 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.62 % Allowed : 6.07 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.28 (0.52), residues: 95 loop : -0.89 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.014 0.002 TYR A 66 PHE 0.015 0.002 PHE A 121 TRP 0.013 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 2429) covalent geometry : angle 0.60654 ( 3311) SS BOND : bond 0.00529 ( 3) SS BOND : angle 3.07167 ( 6) hydrogen bonds : bond 0.04068 ( 69) hydrogen bonds : angle 7.01785 ( 177) link_ALPHA1-3 : bond 0.00768 ( 1) link_ALPHA1-3 : angle 1.36265 ( 3) link_ALPHA1-6 : bond 0.01215 ( 1) link_ALPHA1-6 : angle 1.03571 ( 3) link_BETA1-4 : bond 0.00177 ( 4) link_BETA1-4 : angle 1.82469 ( 12) link_NAG-ASN : bond 0.00415 ( 7) link_NAG-ASN : angle 1.76422 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.065 Fit side-chains REVERT: A 54 ARG cc_start: 0.9230 (mtt180) cc_final: 0.7311 (mmm-85) REVERT: A 115 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8291 (mmtm) REVERT: A 247 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8564 (m) outliers start: 4 outliers final: 1 residues processed: 27 average time/residue: 0.7796 time to fit residues: 21.3508 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.082817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.068462 restraints weight = 3134.094| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.93 r_work: 0.2724 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2445 Z= 0.186 Angle : 0.637 5.347 3356 Z= 0.327 Chirality : 0.045 0.248 406 Planarity : 0.004 0.039 393 Dihedral : 9.277 66.847 566 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.21 % Allowed : 6.48 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.12 (0.56), residues: 86 loop : -0.76 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.014 0.002 TYR A 66 PHE 0.015 0.002 PHE A 121 TRP 0.012 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 2429) covalent geometry : angle 0.60382 ( 3311) SS BOND : bond 0.00443 ( 3) SS BOND : angle 2.61315 ( 6) hydrogen bonds : bond 0.04011 ( 69) hydrogen bonds : angle 7.03920 ( 177) link_ALPHA1-3 : bond 0.00729 ( 1) link_ALPHA1-3 : angle 1.35140 ( 3) link_ALPHA1-6 : bond 0.01253 ( 1) link_ALPHA1-6 : angle 1.02198 ( 3) link_BETA1-4 : bond 0.00178 ( 4) link_BETA1-4 : angle 1.83776 ( 12) link_NAG-ASN : bond 0.00449 ( 7) link_NAG-ASN : angle 1.75360 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.057 Fit side-chains REVERT: A 54 ARG cc_start: 0.9231 (mtt180) cc_final: 0.7299 (mmm-85) REVERT: A 115 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8281 (mmtm) REVERT: A 247 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8582 (m) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.5910 time to fit residues: 15.6098 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.084350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.070024 restraints weight = 3161.334| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.93 r_work: 0.2750 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2445 Z= 0.143 Angle : 0.593 4.712 3356 Z= 0.305 Chirality : 0.044 0.252 406 Planarity : 0.004 0.039 393 Dihedral : 8.832 62.717 566 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.21 % Allowed : 7.69 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.12 (0.56), residues: 86 loop : -0.81 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.013 0.001 TYR A 66 PHE 0.014 0.002 PHE A 121 TRP 0.012 0.001 TRP A 174 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2429) covalent geometry : angle 0.56375 ( 3311) SS BOND : bond 0.00357 ( 3) SS BOND : angle 2.14831 ( 6) hydrogen bonds : bond 0.03748 ( 69) hydrogen bonds : angle 6.95301 ( 177) link_ALPHA1-3 : bond 0.00786 ( 1) link_ALPHA1-3 : angle 1.45705 ( 3) link_ALPHA1-6 : bond 0.01328 ( 1) link_ALPHA1-6 : angle 0.95585 ( 3) link_BETA1-4 : bond 0.00209 ( 4) link_BETA1-4 : angle 1.64919 ( 12) link_NAG-ASN : bond 0.00335 ( 7) link_NAG-ASN : angle 1.64024 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.071 Fit side-chains REVERT: A 54 ARG cc_start: 0.9221 (mtt180) cc_final: 0.7301 (mmm-85) REVERT: A 115 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8289 (mmtm) REVERT: A 247 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8579 (m) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.7182 time to fit residues: 19.6943 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.0670 chunk 18 optimal weight: 0.3980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.083831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.069563 restraints weight = 3133.904| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.91 r_work: 0.2744 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2445 Z= 0.161 Angle : 0.605 4.795 3356 Z= 0.311 Chirality : 0.045 0.257 406 Planarity : 0.004 0.040 393 Dihedral : 8.760 61.674 566 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.21 % Allowed : 8.10 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.13 (0.56), residues: 86 loop : -0.82 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.013 0.001 TYR A 66 PHE 0.014 0.002 PHE A 121 TRP 0.011 0.001 TRP A 174 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2429) covalent geometry : angle 0.57536 ( 3311) SS BOND : bond 0.00456 ( 3) SS BOND : angle 2.30214 ( 6) hydrogen bonds : bond 0.03812 ( 69) hydrogen bonds : angle 7.00258 ( 177) link_ALPHA1-3 : bond 0.00783 ( 1) link_ALPHA1-3 : angle 1.46807 ( 3) link_ALPHA1-6 : bond 0.01294 ( 1) link_ALPHA1-6 : angle 0.94687 ( 3) link_BETA1-4 : bond 0.00206 ( 4) link_BETA1-4 : angle 1.69504 ( 12) link_NAG-ASN : bond 0.00368 ( 7) link_NAG-ASN : angle 1.65223 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.067 Fit side-chains REVERT: A 54 ARG cc_start: 0.9219 (mtt180) cc_final: 0.7309 (mmm-85) REVERT: A 115 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8260 (mmtm) REVERT: A 247 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8592 (m) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.8237 time to fit residues: 21.7397 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 11 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3054 r_free = 0.3054 target = 0.082496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.068091 restraints weight = 3197.184| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.94 r_work: 0.2717 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2445 Z= 0.203 Angle : 0.643 4.923 3356 Z= 0.330 Chirality : 0.046 0.265 406 Planarity : 0.004 0.040 393 Dihedral : 8.921 62.522 566 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.21 % Allowed : 8.10 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.50), residues: 266 helix: None (None), residues: 0 sheet: 0.13 (0.56), residues: 86 loop : -0.83 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.014 0.002 TYR A 66 PHE 0.015 0.002 PHE A 18 TRP 0.011 0.001 TRP A 174 HIS 0.001 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 2429) covalent geometry : angle 0.61160 ( 3311) SS BOND : bond 0.00589 ( 3) SS BOND : angle 2.39207 ( 6) hydrogen bonds : bond 0.04000 ( 69) hydrogen bonds : angle 7.12712 ( 177) link_ALPHA1-3 : bond 0.00745 ( 1) link_ALPHA1-3 : angle 1.41035 ( 3) link_ALPHA1-6 : bond 0.01245 ( 1) link_ALPHA1-6 : angle 0.97691 ( 3) link_BETA1-4 : bond 0.00194 ( 4) link_BETA1-4 : angle 1.82485 ( 12) link_NAG-ASN : bond 0.00478 ( 7) link_NAG-ASN : angle 1.74389 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.088 Fit side-chains REVERT: A 54 ARG cc_start: 0.9231 (mtt180) cc_final: 0.7292 (mmm-85) REVERT: A 247 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8620 (m) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.8559 time to fit residues: 22.6157 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.3091 r_free = 0.3091 target = 0.084090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.069787 restraints weight = 3160.608| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.93 r_work: 0.2760 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2445 Z= 0.154 Angle : 0.597 4.767 3356 Z= 0.308 Chirality : 0.044 0.258 406 Planarity : 0.004 0.040 393 Dihedral : 8.604 59.530 566 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.21 % Allowed : 8.50 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.12 (0.56), residues: 86 loop : -0.83 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.013 0.001 TYR A 66 PHE 0.013 0.002 PHE A 121 TRP 0.012 0.001 TRP A 174 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2429) covalent geometry : angle 0.56893 ( 3311) SS BOND : bond 0.00427 ( 3) SS BOND : angle 2.03785 ( 6) hydrogen bonds : bond 0.03768 ( 69) hydrogen bonds : angle 7.02908 ( 177) link_ALPHA1-3 : bond 0.00731 ( 1) link_ALPHA1-3 : angle 1.46411 ( 3) link_ALPHA1-6 : bond 0.01316 ( 1) link_ALPHA1-6 : angle 0.96633 ( 3) link_BETA1-4 : bond 0.00204 ( 4) link_BETA1-4 : angle 1.63192 ( 12) link_NAG-ASN : bond 0.00341 ( 7) link_NAG-ASN : angle 1.63826 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.096 Fit side-chains REVERT: A 54 ARG cc_start: 0.9232 (mtt180) cc_final: 0.7382 (mmm-85) REVERT: A 115 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8225 (mmtm) REVERT: A 247 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8685 (m) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.9175 time to fit residues: 25.1731 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3067 r_free = 0.3067 target = 0.082617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.068275 restraints weight = 3217.009| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.94 r_work: 0.2734 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2445 Z= 0.201 Angle : 0.638 4.992 3356 Z= 0.328 Chirality : 0.046 0.269 406 Planarity : 0.004 0.041 393 Dihedral : 8.766 60.407 566 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.81 % Allowed : 8.91 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.50), residues: 266 helix: None (None), residues: 0 sheet: 0.14 (0.56), residues: 86 loop : -0.83 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.014 0.002 TYR A 66 PHE 0.015 0.002 PHE A 18 TRP 0.011 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 2429) covalent geometry : angle 0.60748 ( 3311) SS BOND : bond 0.00488 ( 3) SS BOND : angle 2.28257 ( 6) hydrogen bonds : bond 0.03984 ( 69) hydrogen bonds : angle 7.12317 ( 177) link_ALPHA1-3 : bond 0.00654 ( 1) link_ALPHA1-3 : angle 1.38903 ( 3) link_ALPHA1-6 : bond 0.01272 ( 1) link_ALPHA1-6 : angle 1.00448 ( 3) link_BETA1-4 : bond 0.00209 ( 4) link_BETA1-4 : angle 1.80330 ( 12) link_NAG-ASN : bond 0.00471 ( 7) link_NAG-ASN : angle 1.74227 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1379.80 seconds wall clock time: 24 minutes 11.72 seconds (1451.72 seconds total)