Starting phenix.real_space_refine on Wed Aug 5 08:16:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmk_60250/08_2026/8zmk_60250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmk_60250/08_2026/8zmk_60250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zmk_60250/08_2026/8zmk_60250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmk_60250/08_2026/8zmk_60250.map" model { file = "/net/cci-nas-00/data/ceres_data/8zmk_60250/08_2026/8zmk_60250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmk_60250/08_2026/8zmk_60250.cif" } resolution = 3.85 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= 0.008 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: 5 Type Number sf(0) Gaussians P 168 5.49 5 S 40 5.16 5 C 5178 2.51 5 N 1593 2.21 5 O 2225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 9204 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2805 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "C" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 3594 Classifications: {'RNA': 169} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 78, 'rna3p_pyr': 74} Link IDs: {'rna2p': 17, 'rna3p': 151} Restraints were copied for chains: B Time building chain proxies: 2.51, per 1000 atoms: 0.27 Number of scatterers: 9204 At special positions: 0 Unit cell: (91.84, 110.7, 141.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 168 15.00 O 2225 8.00 N 1593 7.00 C 5178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 244.8 milliseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 58.7% alpha, 4.9% beta 55 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 32 through 42 removed outlier: 4.033A pdb=" N GLY A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 109 through 112 Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.730A pdb=" N ILE A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 152 removed outlier: 3.604A pdb=" N ALA A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 189 through 205 Proline residue: A 195 - end of helix removed outlier: 4.155A pdb=" N ILE A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 203 " --> pdb=" O CYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 289 through 298 removed outlier: 4.338A pdb=" N GLU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.505A pdb=" N PHE A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 336 through 362 Proline residue: A 342 - end of helix Proline residue: A 354 - end of helix Processing helix chain 'A' and resid 362 through 373 removed outlier: 3.742A pdb=" N LYS A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 42 removed outlier: 4.034A pdb=" N GLY B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 109 through 112 Processing helix chain 'B' and resid 113 through 131 removed outlier: 3.730A pdb=" N ILE B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 removed outlier: 3.605A pdb=" N ALA B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 166 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 189 through 205 Proline residue: B 195 - end of helix removed outlier: 4.155A pdb=" N ILE B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B 203 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 231 Processing helix chain 'B' and resid 268 through 277 Processing helix chain 'B' and resid 289 through 298 removed outlier: 4.338A pdb=" N GLU B 293 " --> pdb=" O ASN B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.504A pdb=" N PHE B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 336 through 362 Proline residue: B 342 - end of helix Proline residue: B 354 - end of helix Processing helix chain 'B' and resid 362 through 373 removed outlier: 3.743A pdb=" N LYS B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 66 removed outlier: 3.928A pdb=" N ASP A 65 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TRP A 98 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.565A pdb=" N LYS A 318 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 66 removed outlier: 3.927A pdb=" N ASP B 65 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TRP B 98 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 306 through 308 removed outlier: 3.564A pdb=" N LYS B 318 " --> pdb=" O VAL B 308 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.07 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: 2208 1.34 - 1.45: 2687 1.45 - 1.57: 4447 1.57 - 1.69: 336 1.69 - 1.81: 60 Bond restraints: 9738 Sorted by residual: bond pdb=" N9 G C 60 " pdb=" C4 G C 60 " ideal model delta sigma weight residual 1.375 1.388 -0.013 8.00e-03 1.56e+04 2.61e+00 bond pdb=" C5 C C 54 " pdb=" C6 C C 54 " ideal model delta sigma weight residual 1.339 1.329 0.010 8.00e-03 1.56e+04 1.45e+00 bond pdb=" N9 A C 105 " pdb=" C4 A C 105 " ideal model delta sigma weight residual 1.374 1.381 -0.007 6.00e-03 2.78e+04 1.34e+00 bond pdb=" N9 G C 122 " pdb=" C4 G C 122 " ideal model delta sigma weight residual 1.375 1.384 -0.009 8.00e-03 1.56e+04 1.21e+00 bond pdb=" N9 G C 96 " pdb=" C4 G C 96 " ideal model delta sigma weight residual 1.375 1.384 -0.009 8.00e-03 1.56e+04 1.17e+00 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 13006 0.99 - 1.99: 412 1.99 - 2.98: 499 2.98 - 3.98: 20 3.98 - 4.97: 16 Bond angle restraints: 13953 Sorted by residual: angle pdb=" O2 C C 112 " pdb=" C2 C C 112 " pdb=" N3 C C 112 " ideal model delta sigma weight residual 121.90 116.98 4.92 7.00e-01 2.04e+00 4.93e+01 angle pdb=" N1 C C 112 " pdb=" C2 C C 112 " pdb=" O2 C C 112 " ideal model delta sigma weight residual 118.90 122.34 -3.44 6.00e-01 2.78e+00 3.29e+01 angle pdb=" C1' C C 54 " pdb=" N1 C C 54 " pdb=" C2 C C 54 " ideal model delta sigma weight residual 118.80 123.24 -4.44 1.10e+00 8.26e-01 1.63e+01 angle pdb=" O5' C C 54 " pdb=" C5' C C 54 " pdb=" C4' C C 54 " ideal model delta sigma weight residual 109.40 112.59 -3.19 8.00e-01 1.56e+00 1.59e+01 angle pdb=" O5' U C 80 " pdb=" C5' U C 80 " pdb=" C4' U C 80 " ideal model delta sigma weight residual 109.40 112.53 -3.13 8.00e-01 1.56e+00 1.53e+01 ... (remaining 13948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 5438 21.06 - 42.12: 382 42.12 - 63.18: 229 63.18 - 84.25: 98 84.25 - 105.31: 7 Dihedral angle restraints: 6154 sinusoidal: 4116 harmonic: 2038 Sorted by residual: dihedral pdb=" O4' C C 68 " pdb=" C1' C C 68 " pdb=" N1 C C 68 " pdb=" C2 C C 68 " ideal model delta sinusoidal sigma weight residual -160.00 -60.54 -99.46 1 1.50e+01 4.44e-03 4.97e+01 dihedral pdb=" O4' A C 72 " pdb=" C1' A C 72 " pdb=" N9 A C 72 " pdb=" C4 A C 72 " ideal model delta sinusoidal sigma weight residual -106.00 -159.32 53.32 1 1.70e+01 3.46e-03 1.34e+01 dihedral pdb=" O4' G C 95 " pdb=" C1' G C 95 " pdb=" N9 G C 95 " pdb=" C4 G C 95 " ideal model delta sinusoidal sigma weight residual -106.00 -154.18 48.18 1 1.70e+01 3.46e-03 1.11e+01 ... (remaining 6151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1197 0.030 - 0.061: 227 0.061 - 0.091: 66 0.091 - 0.121: 30 0.121 - 0.151: 154 Chirality restraints: 1674 Sorted by residual: chirality pdb=" C2' U C 20 " pdb=" C3' U C 20 " pdb=" O2' U C 20 " pdb=" C1' U C 20 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" C2' C C 98 " pdb=" C3' C C 98 " pdb=" O2' C C 98 " pdb=" C1' C C 98 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" C2' U C 43 " pdb=" C3' U C 43 " pdb=" O2' U C 43 " pdb=" C1' U C 43 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 1671 not shown) Planarity restraints: 1157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 112 " -0.001 2.00e-02 2.50e+03 1.07e-02 2.59e+00 pdb=" N1 C C 112 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C C 112 " 0.027 2.00e-02 2.50e+03 pdb=" O2 C C 112 " -0.015 2.00e-02 2.50e+03 pdb=" N3 C C 112 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C C 112 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 112 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C C 112 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C C 112 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 97 " -0.010 2.00e-02 2.50e+03 7.94e-03 1.89e+00 pdb=" N9 G C 97 " 0.015 2.00e-02 2.50e+03 pdb=" C8 G C 97 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G C 97 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 97 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G C 97 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G C 97 " 0.000 2.00e-02 2.50e+03 pdb=" N1 G C 97 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G C 97 " -0.015 2.00e-02 2.50e+03 pdb=" N2 G C 97 " 0.012 2.00e-02 2.50e+03 pdb=" N3 G C 97 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G C 97 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 98 " -0.017 2.00e-02 2.50e+03 8.13e-03 1.49e+00 pdb=" N1 C C 98 " 0.014 2.00e-02 2.50e+03 pdb=" C2 C C 98 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C C 98 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C C 98 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C C 98 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C C 98 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C C 98 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C C 98 " 0.003 2.00e-02 2.50e+03 ... (remaining 1154 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1173 2.75 - 3.29: 8617 3.29 - 3.83: 16460 3.83 - 4.36: 19113 4.36 - 4.90: 29367 Nonbonded interactions: 74730 Sorted by model distance: nonbonded pdb=" O2' G C 73 " pdb=" O2' U C 125 " model vdw 2.215 3.040 nonbonded pdb=" N4 C C 1 " pdb=" O6 G C 2 " model vdw 2.247 3.120 nonbonded pdb=" O2 U C 43 " pdb=" O6 G C 122 " model vdw 2.258 2.432 nonbonded pdb=" OD1 ASP B 101 " pdb=" OG SER B 145 " model vdw 2.271 3.040 nonbonded pdb=" OD1 ASP A 101 " pdb=" OG SER A 145 " model vdw 2.272 3.040 ... (remaining 74725 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 'A' selection = chain 'B' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3317 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 : 0.002 0.037 9738 Z= 0.131 Angle : 0.609 4.969 13953 Z= 0.488 Chirality : 0.050 0.151 1674 Planarity : 0.003 0.027 1157 Dihedral : 18.722 105.308 4834 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.37 % Favored : 89.05 % Rotamer: Outliers : 2.27 % Allowed : 3.56 % Favored : 94.17 % 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: -2.54 (0.28), residues: 694 helix: -0.84 (0.25), residues: 384 sheet: -2.71 (0.66), residues: 46 loop : -2.68 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 371 TYR 0.003 0.001 TYR B 226 PHE 0.004 0.001 PHE A 203 TRP 0.002 0.000 TRP B 128 HIS 0.001 0.000 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.13 ( 9738) covalent geometry : angle 0.60901 / 0.49 (13953) hydrogen bonds : bond 0.13572 / 8.58 ( 392) hydrogen bonds : angle 4.84441 / 3.37 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7275 (tt) cc_final: 0.6686 (tt) REVERT: A 317 ASN cc_start: 0.7327 (m-40) cc_final: 0.7098 (m-40) REVERT: B 33 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5897 (pm20) REVERT: B 254 MET cc_start: 0.1854 (mmp) cc_final: 0.1432 (mmp) REVERT: B 327 ILE cc_start: 0.6261 (mm) cc_final: 0.6004 (tp) outliers start: 14 outliers final: 3 residues processed: 188 average time/residue: 0.1227 time to fit residues: 30.0009 Evaluate side-chains 110 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 147 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 165 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.181598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.164315 restraints weight = 74309.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.166500 restraints weight = 52092.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.167937 restraints weight = 41437.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.168916 restraints weight = 35300.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.169564 restraints weight = 31386.565| |-----------------------------------------------------------------------------| r_work (final): 0.4704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9738 Z= 0.151 Angle : 0.660 11.951 13953 Z= 0.339 Chirality : 0.038 0.355 1674 Planarity : 0.005 0.031 1157 Dihedral : 21.196 104.133 3372 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.75 % Allowed : 14.56 % Favored : 82.69 % 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: -1.66 (0.30), residues: 694 helix: -0.14 (0.27), residues: 382 sheet: -1.44 (0.88), residues: 32 loop : -2.43 (0.30), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 94 TYR 0.023 0.003 TYR B 323 PHE 0.033 0.003 PHE B 359 TRP 0.008 0.001 TRP B 144 HIS 0.019 0.003 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9738) covalent geometry : angle 0.65983 / 0.34 (13953) hydrogen bonds : bond 0.05421 / 3.75 ( 392) hydrogen bonds : angle 4.18712 / 2.94 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.4617 (mmp) cc_final: 0.4027 (mmt) REVERT: A 203 PHE cc_start: 0.7599 (t80) cc_final: 0.7380 (m-80) REVERT: A 263 VAL cc_start: 0.8608 (t) cc_final: 0.8402 (p) REVERT: A 265 MET cc_start: 0.8277 (mmm) cc_final: 0.7749 (mmm) REVERT: A 317 ASN cc_start: 0.9308 (m-40) cc_final: 0.8949 (m-40) REVERT: B 33 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8973 (pm20) REVERT: B 81 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8921 (mmmt) REVERT: B 88 LEU cc_start: 0.6486 (mt) cc_final: 0.6256 (pp) REVERT: B 254 MET cc_start: 0.5305 (mmp) cc_final: 0.3361 (mmp) outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 0.1117 time to fit residues: 18.4493 Evaluate side-chains 107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 73 optimal weight: 40.0000 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 30.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 220 ASN ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.163257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.145142 restraints weight = 74571.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.147571 restraints weight = 63017.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.148809 restraints weight = 44398.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.148887 restraints weight = 37197.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.149025 restraints weight = 36946.335| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 9738 Z= 0.324 Angle : 0.886 10.544 13953 Z= 0.473 Chirality : 0.045 0.303 1674 Planarity : 0.007 0.053 1157 Dihedral : 21.739 101.538 3372 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 5.34 % Allowed : 13.92 % Favored : 80.74 % 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: -2.36 (0.29), residues: 694 helix: -0.76 (0.26), residues: 384 sheet: -2.27 (0.79), residues: 44 loop : -2.58 (0.30), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 310 TYR 0.039 0.003 TYR B 294 PHE 0.036 0.005 PHE A 264 TRP 0.026 0.003 TRP B 302 HIS 0.015 0.003 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.32 ( 9738) covalent geometry : angle 0.88597 / 0.47 (13953) hydrogen bonds : bond 0.11678 / 7.90 ( 392) hydrogen bonds : angle 4.92007 / 3.33 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TRP cc_start: 0.7844 (m-10) cc_final: 0.7605 (m-10) REVERT: A 133 MET cc_start: 0.5413 (mmp) cc_final: 0.4587 (mmm) REVERT: A 243 MET cc_start: 0.8789 (pmm) cc_final: 0.8537 (tpp) REVERT: A 265 MET cc_start: 0.8792 (mmm) cc_final: 0.8447 (mmm) REVERT: A 269 GLU cc_start: 0.9288 (tt0) cc_final: 0.8944 (tm-30) REVERT: A 346 LYS cc_start: 0.9272 (tppt) cc_final: 0.9050 (tptp) REVERT: B 33 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.9063 (pm20) REVERT: B 38 VAL cc_start: 0.9429 (t) cc_final: 0.9199 (m) REVERT: B 62 VAL cc_start: 0.8838 (t) cc_final: 0.8179 (t) REVERT: B 81 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9120 (mmmt) REVERT: B 113 ASP cc_start: 0.9002 (t0) cc_final: 0.8709 (t0) REVERT: B 116 LYS cc_start: 0.9324 (mtpt) cc_final: 0.9095 (mtpt) REVERT: B 228 ASP cc_start: 0.8649 (m-30) cc_final: 0.8392 (m-30) REVERT: B 229 ASP cc_start: 0.8582 (m-30) cc_final: 0.8370 (m-30) REVERT: B 254 MET cc_start: 0.5113 (OUTLIER) cc_final: 0.4396 (mmp) REVERT: B 294 TYR cc_start: 0.8212 (m-10) cc_final: 0.7937 (m-80) REVERT: B 295 ILE cc_start: 0.9269 (tp) cc_final: 0.8708 (pt) outliers start: 33 outliers final: 21 residues processed: 122 average time/residue: 0.0914 time to fit residues: 15.3770 Evaluate side-chains 105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 17 optimal weight: 0.1980 chunk 1 optimal weight: 0.0010 chunk 72 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 86 ASN B 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.169880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5129 r_free = 0.5129 target = 0.152809 restraints weight = 74688.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.155173 restraints weight = 59811.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.156367 restraints weight = 42004.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.156475 restraints weight = 35765.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.156623 restraints weight = 35365.641| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9738 Z= 0.139 Angle : 0.635 14.109 13953 Z= 0.325 Chirality : 0.037 0.379 1674 Planarity : 0.005 0.086 1157 Dihedral : 21.740 102.589 3367 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.69 % Allowed : 16.99 % Favored : 78.32 % 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: -1.70 (0.31), residues: 694 helix: -0.22 (0.27), residues: 386 sheet: -2.65 (0.72), residues: 46 loop : -2.14 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 39 TYR 0.019 0.002 TYR A 123 PHE 0.031 0.003 PHE B 35 TRP 0.007 0.001 TRP B 98 HIS 0.010 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9738) covalent geometry : angle 0.63535 / 0.32 (13953) hydrogen bonds : bond 0.06121 / 4.14 ( 392) hydrogen bonds : angle 4.51386 / 3.10 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.3197 (ttt) cc_final: 0.2578 (ttt) REVERT: A 113 ASP cc_start: 0.8695 (t0) cc_final: 0.8402 (t0) REVERT: A 133 MET cc_start: 0.5196 (OUTLIER) cc_final: 0.4359 (mmm) REVERT: A 254 MET cc_start: 0.6207 (mmm) cc_final: 0.5449 (mmm) REVERT: A 346 LYS cc_start: 0.9279 (tppt) cc_final: 0.8971 (tptp) REVERT: B 33 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.8986 (pm20) REVERT: B 58 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5924 (pttp) REVERT: B 62 VAL cc_start: 0.8754 (t) cc_final: 0.8503 (t) REVERT: B 133 MET cc_start: 0.5312 (ptm) cc_final: 0.4645 (ptt) REVERT: B 179 MET cc_start: 0.6586 (ttt) cc_final: 0.6384 (ttm) REVERT: B 228 ASP cc_start: 0.8453 (m-30) cc_final: 0.8159 (m-30) REVERT: B 229 ASP cc_start: 0.8374 (m-30) cc_final: 0.8126 (m-30) REVERT: B 254 MET cc_start: 0.5327 (OUTLIER) cc_final: 0.4565 (mmp) outliers start: 29 outliers final: 16 residues processed: 114 average time/residue: 0.1037 time to fit residues: 16.1364 Evaluate side-chains 107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.167595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.150392 restraints weight = 73546.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.153017 restraints weight = 64268.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.154095 restraints weight = 42299.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.154180 restraints weight = 36340.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.154271 restraints weight = 35351.271| |-----------------------------------------------------------------------------| r_work (final): 0.4516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9738 Z= 0.145 Angle : 0.613 14.927 13953 Z= 0.313 Chirality : 0.037 0.397 1674 Planarity : 0.007 0.162 1157 Dihedral : 21.711 102.572 3367 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.37 % Allowed : 17.48 % Favored : 78.16 % 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: -1.52 (0.31), residues: 694 helix: -0.04 (0.27), residues: 386 sheet: -2.70 (0.71), residues: 46 loop : -2.09 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.019 0.002 TYR A 123 PHE 0.031 0.003 PHE A 203 TRP 0.007 0.001 TRP A 157 HIS 0.008 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 9738) covalent geometry : angle 0.61333 / 0.31 (13953) hydrogen bonds : bond 0.05813 / 3.92 ( 392) hydrogen bonds : angle 4.64102 / 3.17 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.5287 (OUTLIER) cc_final: 0.4455 (mmm) REVERT: A 166 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8611 (ttmm) REVERT: A 179 MET cc_start: 0.5497 (tpp) cc_final: 0.5196 (tpp) REVERT: A 254 MET cc_start: 0.5936 (mmm) cc_final: 0.5510 (mmm) REVERT: A 265 MET cc_start: 0.8657 (mmm) cc_final: 0.8299 (mmm) REVERT: A 346 LYS cc_start: 0.9329 (tppt) cc_final: 0.9002 (tptp) REVERT: B 54 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9126 (pp) REVERT: B 77 GLN cc_start: 0.8994 (pt0) cc_final: 0.8700 (pm20) REVERT: B 86 ASN cc_start: 0.9049 (m110) cc_final: 0.8704 (p0) REVERT: B 122 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.8004 (mmm160) REVERT: B 133 MET cc_start: 0.5747 (ptm) cc_final: 0.5416 (ptt) REVERT: B 201 ASP cc_start: 0.8725 (m-30) cc_final: 0.8168 (t0) REVERT: B 205 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8961 (mt) REVERT: B 228 ASP cc_start: 0.8485 (m-30) cc_final: 0.8194 (m-30) REVERT: B 229 ASP cc_start: 0.8396 (m-30) cc_final: 0.8142 (m-30) REVERT: B 254 MET cc_start: 0.5463 (mmp) cc_final: 0.4970 (mmp) REVERT: B 294 TYR cc_start: 0.7428 (m-80) cc_final: 0.7082 (m-80) outliers start: 27 outliers final: 15 residues processed: 114 average time/residue: 0.0924 time to fit residues: 14.5603 Evaluate side-chains 105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 40.0000 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.168999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.152081 restraints weight = 73813.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.154481 restraints weight = 62255.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.155734 restraints weight = 41830.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.155761 restraints weight = 35593.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.155904 restraints weight = 34987.946| |-----------------------------------------------------------------------------| r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9738 Z= 0.125 Angle : 0.614 14.274 13953 Z= 0.308 Chirality : 0.036 0.388 1674 Planarity : 0.005 0.087 1157 Dihedral : 21.613 102.436 3364 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.07 % Allowed : 19.26 % Favored : 77.67 % 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: -1.48 (0.31), residues: 694 helix: 0.01 (0.27), residues: 388 sheet: -2.63 (0.72), residues: 46 loop : -2.13 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 39 TYR 0.028 0.002 TYR A 64 PHE 0.028 0.003 PHE B 35 TRP 0.014 0.001 TRP B 302 HIS 0.008 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9738) covalent geometry : angle 0.61357 / 0.31 (13953) hydrogen bonds : bond 0.05141 / 3.42 ( 392) hydrogen bonds : angle 4.68331 / 3.24 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.5127 (mmp) cc_final: 0.4291 (mmm) REVERT: A 254 MET cc_start: 0.5465 (mmm) cc_final: 0.5126 (mmm) REVERT: A 265 MET cc_start: 0.8614 (mmm) cc_final: 0.8258 (mmm) REVERT: A 297 TYR cc_start: 0.8635 (m-80) cc_final: 0.7514 (t80) REVERT: A 346 LYS cc_start: 0.9292 (tppt) cc_final: 0.8944 (tptp) REVERT: B 86 ASN cc_start: 0.9025 (m110) cc_final: 0.8641 (p0) REVERT: B 133 MET cc_start: 0.5604 (ptm) cc_final: 0.5334 (ptt) REVERT: B 162 ASP cc_start: 0.9136 (t0) cc_final: 0.8906 (t0) REVERT: B 201 ASP cc_start: 0.8571 (m-30) cc_final: 0.8047 (t0) REVERT: B 228 ASP cc_start: 0.8433 (m-30) cc_final: 0.8129 (m-30) REVERT: B 229 ASP cc_start: 0.8327 (m-30) cc_final: 0.8051 (m-30) REVERT: B 254 MET cc_start: 0.5334 (OUTLIER) cc_final: 0.4931 (mmp) REVERT: B 294 TYR cc_start: 0.7537 (m-80) cc_final: 0.7156 (m-80) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 0.0870 time to fit residues: 12.9572 Evaluate side-chains 97 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** 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 = 0.4946 r_free = 0.4946 target = 0.167792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.150701 restraints weight = 73683.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.153237 restraints weight = 63963.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.154571 restraints weight = 41916.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.154585 restraints weight = 35711.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.154714 restraints weight = 34760.261| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9738 Z= 0.132 Angle : 0.636 12.824 13953 Z= 0.322 Chirality : 0.036 0.380 1674 Planarity : 0.005 0.071 1157 Dihedral : 21.596 102.040 3364 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.40 % Allowed : 19.42 % Favored : 77.18 % 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: -1.41 (0.31), residues: 694 helix: 0.03 (0.27), residues: 390 sheet: -2.62 (0.72), residues: 46 loop : -2.04 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 39 TYR 0.026 0.002 TYR A 64 PHE 0.026 0.003 PHE B 204 TRP 0.008 0.001 TRP B 98 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9738) covalent geometry : angle 0.63647 / 0.32 (13953) hydrogen bonds : bond 0.05592 / 3.86 ( 392) hydrogen bonds : angle 4.67508 / 3.19 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4181 (mmt) REVERT: A 179 MET cc_start: 0.5168 (tpp) cc_final: 0.4928 (tpp) REVERT: A 243 MET cc_start: 0.8885 (pmm) cc_final: 0.8404 (mpp) REVERT: A 254 MET cc_start: 0.5679 (mmm) cc_final: 0.5391 (mmm) REVERT: A 265 MET cc_start: 0.8722 (mmm) cc_final: 0.8422 (mmm) REVERT: A 269 GLU cc_start: 0.9217 (tt0) cc_final: 0.8833 (tm-30) REVERT: A 346 LYS cc_start: 0.9353 (tppt) cc_final: 0.8992 (tptp) REVERT: B 109 LYS cc_start: 0.5228 (tptt) cc_final: 0.4703 (tptt) REVERT: B 110 MET cc_start: 0.7124 (pmm) cc_final: 0.6525 (pmm) REVERT: B 162 ASP cc_start: 0.9176 (t0) cc_final: 0.8943 (t0) REVERT: B 228 ASP cc_start: 0.8503 (m-30) cc_final: 0.8201 (m-30) REVERT: B 229 ASP cc_start: 0.8377 (m-30) cc_final: 0.8099 (m-30) REVERT: B 254 MET cc_start: 0.5438 (OUTLIER) cc_final: 0.5071 (mmp) REVERT: B 294 TYR cc_start: 0.7625 (m-80) cc_final: 0.7350 (m-80) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.0923 time to fit residues: 13.6421 Evaluate side-chains 103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 73 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** 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 = 0.4845 r_free = 0.4845 target = 0.158014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.139875 restraints weight = 74389.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.142326 restraints weight = 67948.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.143557 restraints weight = 44608.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.143558 restraints weight = 37914.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.143726 restraints weight = 37324.839| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9738 Z= 0.246 Angle : 0.745 14.542 13953 Z= 0.390 Chirality : 0.041 0.308 1674 Planarity : 0.006 0.079 1157 Dihedral : 21.936 99.615 3364 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 31.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.88 % Allowed : 21.04 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.30), residues: 694 helix: -0.46 (0.26), residues: 388 sheet: -2.73 (0.75), residues: 46 loop : -1.97 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 39 TYR 0.024 0.003 TYR A 123 PHE 0.067 0.005 PHE B 359 TRP 0.011 0.002 TRP B 302 HIS 0.006 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.25 ( 9738) covalent geometry : angle 0.74532 / 0.39 (13953) hydrogen bonds : bond 0.08885 / 5.98 ( 392) hydrogen bonds : angle 5.18960 / 3.58 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.4529 (mmt) REVERT: A 166 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8663 (ttmm) REVERT: A 179 MET cc_start: 0.5721 (tpp) cc_final: 0.4811 (tpt) REVERT: A 243 MET cc_start: 0.8862 (pmm) cc_final: 0.8545 (tpp) REVERT: A 254 MET cc_start: 0.6156 (mmm) cc_final: 0.4563 (mmm) REVERT: A 265 MET cc_start: 0.8774 (mmm) cc_final: 0.8556 (mmm) REVERT: A 269 GLU cc_start: 0.9303 (tt0) cc_final: 0.8954 (tm-30) REVERT: A 346 LYS cc_start: 0.9398 (tppt) cc_final: 0.9051 (tptp) REVERT: B 86 ASN cc_start: 0.9109 (m110) cc_final: 0.8860 (p0) REVERT: B 110 MET cc_start: 0.7575 (pmm) cc_final: 0.6889 (pmm) REVERT: B 159 LEU cc_start: 0.9147 (mt) cc_final: 0.8930 (mt) REVERT: B 214 MET cc_start: 0.6858 (pmm) cc_final: 0.6455 (mmm) REVERT: B 228 ASP cc_start: 0.8682 (m-30) cc_final: 0.8285 (m-30) REVERT: B 229 ASP cc_start: 0.8694 (m-30) cc_final: 0.8417 (m-30) REVERT: B 294 TYR cc_start: 0.7728 (m-10) cc_final: 0.7241 (m-80) outliers start: 24 outliers final: 19 residues processed: 106 average time/residue: 0.0908 time to fit residues: 13.2954 Evaluate side-chains 105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 79 optimal weight: 40.0000 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.144661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.117896 restraints weight = 50632.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.120204 restraints weight = 38921.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.121214 restraints weight = 32676.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.121214 restraints weight = 29384.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.121214 restraints weight = 29384.206| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9738 Z= 0.139 Angle : 0.679 14.428 13953 Z= 0.342 Chirality : 0.038 0.439 1674 Planarity : 0.005 0.042 1157 Dihedral : 21.867 100.465 3364 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.56 % Allowed : 21.84 % Favored : 74.60 % 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: -1.53 (0.31), residues: 694 helix: -0.16 (0.27), residues: 388 sheet: -2.58 (0.74), residues: 46 loop : -1.93 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 39 TYR 0.025 0.002 TYR A 64 PHE 0.026 0.003 PHE B 35 TRP 0.010 0.001 TRP B 98 HIS 0.006 0.002 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 9738) covalent geometry : angle 0.67890 / 0.34 (13953) hydrogen bonds : bond 0.05917 / 4.00 ( 392) hydrogen bonds : angle 4.83333 / 3.30 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.5499 (mmm) REVERT: A 179 MET cc_start: 0.5325 (tpp) cc_final: 0.4631 (tpt) REVERT: A 243 MET cc_start: 0.8943 (pmm) cc_final: 0.8424 (mpp) REVERT: A 254 MET cc_start: 0.6373 (mmm) cc_final: 0.6043 (mmm) REVERT: A 265 MET cc_start: 0.8859 (mmm) cc_final: 0.8547 (mmm) REVERT: A 269 GLU cc_start: 0.9324 (tt0) cc_final: 0.8953 (tm-30) REVERT: A 346 LYS cc_start: 0.9354 (tppt) cc_final: 0.8975 (tptp) REVERT: B 50 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8900 (pm20) REVERT: B 81 LYS cc_start: 0.9103 (tptt) cc_final: 0.8798 (mmmt) REVERT: B 110 MET cc_start: 0.7366 (pmm) cc_final: 0.7086 (pmm) REVERT: B 179 MET cc_start: 0.7293 (ttm) cc_final: 0.5119 (tpt) REVERT: B 214 MET cc_start: 0.6767 (pmm) cc_final: 0.6442 (mmm) REVERT: B 228 ASP cc_start: 0.8677 (m-30) cc_final: 0.8279 (m-30) REVERT: B 229 ASP cc_start: 0.8556 (m-30) cc_final: 0.8268 (m-30) REVERT: B 254 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.5012 (mmp) REVERT: B 294 TYR cc_start: 0.7759 (m-10) cc_final: 0.7443 (m-80) outliers start: 22 outliers final: 17 residues processed: 98 average time/residue: 0.0774 time to fit residues: 10.6575 Evaluate side-chains 98 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.145236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.118530 restraints weight = 51000.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.120885 restraints weight = 38728.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.122478 restraints weight = 32527.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.123083 restraints weight = 28771.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.124155 restraints weight = 26971.212| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9738 Z= 0.129 Angle : 0.675 14.982 13953 Z= 0.336 Chirality : 0.037 0.423 1674 Planarity : 0.005 0.055 1157 Dihedral : 21.775 100.910 3364 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.40 % Allowed : 22.49 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.31), residues: 694 helix: -0.11 (0.27), residues: 388 sheet: -2.32 (0.77), residues: 46 loop : -1.91 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 39 TYR 0.024 0.002 TYR A 64 PHE 0.023 0.003 PHE B 35 TRP 0.011 0.001 TRP B 98 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9738) covalent geometry : angle 0.67519 / 0.34 (13953) hydrogen bonds : bond 0.05507 / 3.73 ( 392) hydrogen bonds : angle 4.73981 / 3.27 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5129 (mmm) REVERT: A 166 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8578 (ttmm) REVERT: A 179 MET cc_start: 0.5338 (tpp) cc_final: 0.4655 (tpt) REVERT: A 197 MET cc_start: 0.4462 (tpt) cc_final: 0.4260 (tpp) REVERT: A 243 MET cc_start: 0.8866 (pmm) cc_final: 0.8404 (mpp) REVERT: A 265 MET cc_start: 0.8695 (mmm) cc_final: 0.8461 (mmm) REVERT: A 269 GLU cc_start: 0.9270 (tt0) cc_final: 0.8895 (tm-30) REVERT: A 346 LYS cc_start: 0.9324 (tppt) cc_final: 0.8943 (tptp) REVERT: B 50 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8787 (pm20) REVERT: B 53 ASN cc_start: 0.9369 (m-40) cc_final: 0.9058 (p0) REVERT: B 81 LYS cc_start: 0.9110 (tptt) cc_final: 0.8788 (mmmt) REVERT: B 179 MET cc_start: 0.6898 (ttm) cc_final: 0.4921 (tpt) REVERT: B 214 MET cc_start: 0.6669 (pmm) cc_final: 0.6252 (mmm) REVERT: B 228 ASP cc_start: 0.8600 (m-30) cc_final: 0.8192 (m-30) REVERT: B 229 ASP cc_start: 0.8570 (m-30) cc_final: 0.8280 (m-30) REVERT: B 254 MET cc_start: 0.4986 (OUTLIER) cc_final: 0.4591 (mmp) REVERT: B 294 TYR cc_start: 0.7689 (m-10) cc_final: 0.7357 (m-80) outliers start: 21 outliers final: 15 residues processed: 98 average time/residue: 0.0890 time to fit residues: 12.0768 Evaluate side-chains 102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 83 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.164815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.148989 restraints weight = 73396.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.149949 restraints weight = 55204.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.150947 restraints weight = 44573.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.151012 restraints weight = 38029.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.151456 restraints weight = 37031.287| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9738 Z= 0.124 Angle : 0.664 14.512 13953 Z= 0.332 Chirality : 0.037 0.401 1674 Planarity : 0.004 0.049 1157 Dihedral : 21.691 100.698 3364 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.40 % Allowed : 22.65 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.31), residues: 694 helix: -0.02 (0.27), residues: 388 sheet: -2.20 (0.79), residues: 46 loop : -1.84 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 39 TYR 0.024 0.002 TYR A 64 PHE 0.025 0.003 PHE B 35 TRP 0.013 0.001 TRP B 98 HIS 0.005 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9738) covalent geometry : angle 0.66440 / 0.33 (13953) hydrogen bonds : bond 0.05249 / 3.56 ( 392) hydrogen bonds : angle 4.63691 / 3.20 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.38 seconds wall clock time: 31 minutes 35.19 seconds (1895.19 seconds total)