Starting phenix.real_space_refine on Thu Jul 2 15:18:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmk_60250/07_2026/8zmk_60250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmk_60250/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zmk_60250/07_2026/8zmk_60250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmk_60250/07_2026/8zmk_60250.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zmk_60250/07_2026/8zmk_60250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmk_60250/07_2026/8zmk_60250.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.58, per 1000 atoms: 0.28 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: 0.72 Conformation dependent library (CDL) restraints added in 210.2 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: 1.11 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: 1.37 Time building geometry restraints manager: 0.91 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: 13515 0.99 - 1.99: 336 1.99 - 2.98: 70 2.98 - 3.98: 16 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=" N1 C C 77 " pdb=" C2 C C 77 " pdb=" O2 C C 77 " ideal model delta sigma weight residual 118.90 121.21 -2.31 6.00e-01 2.78e+00 1.49e+01 angle pdb=" C1' C C 54 " pdb=" N1 C C 54 " pdb=" C6 C C 54 " ideal model delta sigma weight residual 120.80 116.73 4.07 1.20e+00 6.94e-01 1.15e+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 - 0.027: 1325 0.027 - 0.053: 228 0.053 - 0.080: 70 0.080 - 0.107: 44 0.107 - 0.134: 7 Chirality restraints: 1674 Sorted by residual: chirality pdb=" CA ILE A 46 " pdb=" N ILE A 46 " pdb=" C ILE A 46 " pdb=" CB ILE A 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE B 97 " pdb=" N ILE B 97 " pdb=" C ILE B 97 " pdb=" CB ILE B 97 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.17e-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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- 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= 0.114 Angle : 0.421 4.969 13953 Z= 0.346 Chirality : 0.028 0.134 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 0.00162 / 0.11 ( 9738) covalent geometry : angle 0.42101 / 0.35 (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 : 0.200 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: 0.5898 (pm20) REVERT: B 254 MET cc_start: 0.1854 (mmp) cc_final: 0.1423 (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: 0.1100 time to fit residues: 26.7556 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 : 0.200 ------------------------------------------------------------------------------- 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: 0.7980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.181534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.164321 restraints weight = 74215.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.166424 restraints weight = 51978.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.167865 restraints weight = 41332.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.168846 restraints weight = 35197.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.169478 restraints weight = 31284.989| |-----------------------------------------------------------------------------| r_work (final): 0.4702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9738 Z= 0.152 Angle : 0.654 11.930 13953 Z= 0.338 Chirality : 0.037 0.378 1674 Planarity : 0.005 0.030 1157 Dihedral : 21.263 106.691 3372 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.59 % Allowed : 14.40 % Favored : 83.01 % 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: -1.64 (0.30), residues: 694 helix: -0.11 (0.27), residues: 382 sheet: -1.42 (0.89), residues: 32 loop : -2.43 (0.30), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 94 TYR 0.023 0.003 TYR B 323 PHE 0.041 0.003 PHE B 359 TRP 0.007 0.002 TRP A 144 HIS 0.019 0.003 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9738) covalent geometry : angle 0.65445 / 0.34 (13953) hydrogen bonds : bond 0.05291 / 3.65 ( 392) hydrogen bonds : angle 4.18981 / 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 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.258 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: symmetry clash REVERT: A 133 MET cc_start: 0.4514 (mmp) cc_final: 0.3883 (mmt) REVERT: A 265 MET cc_start: 0.8279 (mmm) cc_final: 0.7762 (mmm) REVERT: A 317 ASN cc_start: 0.9262 (m-40) cc_final: 0.8889 (m-40) REVERT: B 33 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8926 (pm20) REVERT: B 88 LEU cc_start: 0.6519 (mt) cc_final: 0.6307 (pp) REVERT: B 254 MET cc_start: 0.5207 (mmp) cc_final: 0.3270 (mmp) outliers start: 16 outliers final: 10 residues processed: 128 average time/residue: 0.1039 time to fit residues: 17.4278 Evaluate side-chains 105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 349 ASN 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: 3.9990 chunk 22 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 0.0770 chunk 82 optimal weight: 20.0000 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.170216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.154098 restraints weight = 74491.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.156251 restraints weight = 54384.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.156519 restraints weight = 40434.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.156642 restraints weight = 36373.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.157130 restraints weight = 35204.540| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9738 Z= 0.226 Angle : 0.694 10.305 13953 Z= 0.371 Chirality : 0.037 0.280 1674 Planarity : 0.005 0.041 1157 Dihedral : 21.569 104.864 3372 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.88 % Allowed : 14.56 % Favored : 81.55 % 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: -1.58 (0.31), residues: 694 helix: -0.18 (0.27), residues: 388 sheet: -1.06 (1.05), residues: 32 loop : -2.30 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 232 TYR 0.035 0.003 TYR B 294 PHE 0.029 0.004 PHE A 264 TRP 0.015 0.002 TRP A 302 HIS 0.016 0.003 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 ( 9738) covalent geometry : angle 0.69378 / 0.37 (13953) hydrogen bonds : bond 0.07891 / 5.34 ( 392) hydrogen bonds : angle 4.36606 / 2.95 ( 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 126 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.213 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: A 133 MET cc_start: 0.4864 (mmp) cc_final: 0.4076 (mmm) REVERT: A 179 MET cc_start: 0.6159 (tpp) cc_final: 0.5854 (tpp) REVERT: A 265 MET cc_start: 0.8614 (mmm) cc_final: 0.8277 (mmm) REVERT: A 269 GLU cc_start: 0.9197 (tt0) cc_final: 0.8934 (tt0) REVERT: A 346 LYS cc_start: 0.9248 (tppt) cc_final: 0.9027 (tptp) REVERT: B 38 VAL cc_start: 0.9337 (t) cc_final: 0.8902 (m) REVERT: B 228 ASP cc_start: 0.8348 (m-30) cc_final: 0.8112 (m-30) REVERT: B 229 ASP cc_start: 0.8397 (m-30) cc_final: 0.8189 (m-30) REVERT: B 254 MET cc_start: 0.4707 (OUTLIER) cc_final: 0.3631 (mmp) REVERT: B 294 TYR cc_start: 0.7993 (m-80) cc_final: 0.7699 (m-80) outliers start: 24 outliers final: 15 residues processed: 117 average time/residue: 0.0885 time to fit residues: 14.4319 Evaluate side-chains 105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 286 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 94 ARG 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.0020 chunk 72 optimal weight: 30.0000 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4985 r_free = 0.4985 target = 0.173519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.158016 restraints weight = 74754.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.159231 restraints weight = 51841.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.160064 restraints weight = 42130.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.160202 restraints weight = 36489.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.160540 restraints weight = 35923.640| |-----------------------------------------------------------------------------| r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9738 Z= 0.128 Angle : 0.591 15.186 13953 Z= 0.301 Chirality : 0.034 0.342 1674 Planarity : 0.004 0.040 1157 Dihedral : 21.497 105.294 3369 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.40 % Allowed : 16.18 % Favored : 80.42 % 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: -1.35 (0.31), residues: 694 helix: 0.08 (0.27), residues: 388 sheet: -1.43 (0.99), residues: 32 loop : -2.25 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 39 TYR 0.018 0.002 TYR A 123 PHE 0.026 0.002 PHE B 35 TRP 0.009 0.001 TRP B 98 HIS 0.014 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9738) covalent geometry : angle 0.59095 / 0.30 (13953) hydrogen bonds : bond 0.05233 / 3.52 ( 392) hydrogen bonds : angle 4.22696 / 2.92 ( 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 117 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.222 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: A 133 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.3742 (mmm) REVERT: A 179 MET cc_start: 0.5864 (tpp) cc_final: 0.5639 (tpp) REVERT: A 265 MET cc_start: 0.8385 (mmm) cc_final: 0.8091 (mmm) REVERT: A 268 GLU cc_start: 0.8482 (pm20) cc_final: 0.8095 (pp20) REVERT: A 269 GLU cc_start: 0.9049 (tt0) cc_final: 0.8296 (tm-30) REVERT: A 346 LYS cc_start: 0.9258 (tppt) cc_final: 0.8975 (tptp) REVERT: B 58 LYS cc_start: 0.5225 (OUTLIER) cc_final: 0.4549 (pttm) REVERT: B 133 MET cc_start: 0.4802 (ptm) cc_final: 0.4038 (ptt) REVERT: B 228 ASP cc_start: 0.8208 (m-30) cc_final: 0.7954 (m-30) REVERT: B 229 ASP cc_start: 0.8237 (m-30) cc_final: 0.8002 (m-30) REVERT: B 254 MET cc_start: 0.5031 (OUTLIER) cc_final: 0.4242 (mmp) outliers start: 21 outliers final: 11 residues processed: 111 average time/residue: 0.0860 time to fit residues: 12.9627 Evaluate side-chains 105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 286 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 58 LYS 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 254 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN 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: 0.0870 chunk 83 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN B 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.173588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.158157 restraints weight = 73551.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.159954 restraints weight = 52025.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.160455 restraints weight = 40066.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.160567 restraints weight = 35377.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.161405 restraints weight = 34329.506| |-----------------------------------------------------------------------------| r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9738 Z= 0.120 Angle : 0.581 12.194 13953 Z= 0.293 Chirality : 0.035 0.329 1674 Planarity : 0.004 0.042 1157 Dihedral : 21.443 105.209 3365 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.56 % Allowed : 16.18 % Favored : 80.26 % 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: -1.25 (0.32), residues: 694 helix: 0.20 (0.28), residues: 390 sheet: -2.16 (0.80), residues: 42 loop : -2.16 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 94 TYR 0.019 0.002 TYR A 123 PHE 0.026 0.002 PHE B 35 TRP 0.008 0.001 TRP B 98 HIS 0.009 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9738) covalent geometry : angle 0.58083 / 0.29 (13953) hydrogen bonds : bond 0.04744 / 3.20 ( 392) hydrogen bonds : angle 4.18821 / 2.89 ( 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 119 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.254 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: A 64 TYR cc_start: 0.7702 (p90) cc_final: 0.7411 (p90) REVERT: A 133 MET cc_start: 0.4700 (OUTLIER) cc_final: 0.3820 (mmm) REVERT: A 265 MET cc_start: 0.8508 (mmm) cc_final: 0.8008 (mmm) REVERT: A 269 GLU cc_start: 0.9100 (tt0) cc_final: 0.8701 (tm-30) REVERT: A 294 TYR cc_start: 0.8359 (m-10) cc_final: 0.7846 (m-80) REVERT: A 346 LYS cc_start: 0.9288 (tppt) cc_final: 0.9001 (tptp) REVERT: B 58 LYS cc_start: 0.5020 (OUTLIER) cc_final: 0.4138 (ptmm) REVERT: B 110 MET cc_start: 0.6588 (ptp) cc_final: 0.6116 (pmm) REVERT: B 133 MET cc_start: 0.4995 (ptm) cc_final: 0.4324 (ptt) REVERT: B 228 ASP cc_start: 0.8133 (m-30) cc_final: 0.7869 (m-30) REVERT: B 229 ASP cc_start: 0.8269 (m-30) cc_final: 0.8034 (m-30) REVERT: B 254 MET cc_start: 0.4968 (mmp) cc_final: 0.4122 (mmp) REVERT: B 294 TYR cc_start: 0.7477 (m-80) cc_final: 0.7172 (m-80) outliers start: 22 outliers final: 11 residues processed: 116 average time/residue: 0.0955 time to fit residues: 14.9741 Evaluate side-chains 104 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS 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 308 VAL Chi-restraints excluded: chain B residue 58 LYS 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 242 HIS 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: 2.9990 chunk 72 optimal weight: 30.0000 chunk 47 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN B 198 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.171861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.156280 restraints weight = 74097.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.157900 restraints weight = 53105.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.158463 restraints weight = 41958.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.158656 restraints weight = 36225.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.159807 restraints weight = 35036.245| |-----------------------------------------------------------------------------| r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9738 Z= 0.127 Angle : 0.585 11.842 13953 Z= 0.298 Chirality : 0.035 0.355 1674 Planarity : 0.004 0.044 1157 Dihedral : 21.453 104.619 3364 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.72 % Allowed : 16.50 % Favored : 79.77 % 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: -1.16 (0.32), residues: 694 helix: 0.29 (0.28), residues: 390 sheet: -2.07 (0.81), residues: 42 loop : -2.14 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 94 TYR 0.020 0.002 TYR B 64 PHE 0.029 0.002 PHE B 35 TRP 0.023 0.002 TRP B 302 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9738) covalent geometry : angle 0.58539 / 0.30 (13953) hydrogen bonds : bond 0.04967 / 3.31 ( 392) hydrogen bonds : angle 4.32206 / 3.01 ( 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 122 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.268 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: A 64 TYR cc_start: 0.7659 (p90) cc_final: 0.7386 (p90) REVERT: A 133 MET cc_start: 0.4712 (OUTLIER) cc_final: 0.3837 (mmm) REVERT: A 166 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8505 (ttmt) REVERT: A 265 MET cc_start: 0.8557 (mmm) cc_final: 0.8075 (mmm) REVERT: A 269 GLU cc_start: 0.9108 (tt0) cc_final: 0.8699 (tm-30) REVERT: A 346 LYS cc_start: 0.9287 (tppt) cc_final: 0.8943 (tptp) REVERT: B 86 ASN cc_start: 0.9015 (m110) cc_final: 0.8693 (p0) REVERT: B 110 MET cc_start: 0.6308 (ptp) cc_final: 0.5354 (pmm) REVERT: B 133 MET cc_start: 0.5032 (ptm) cc_final: 0.4744 (ptt) REVERT: B 228 ASP cc_start: 0.8278 (m-30) cc_final: 0.8010 (m-30) REVERT: B 229 ASP cc_start: 0.8352 (m-30) cc_final: 0.8125 (m-30) REVERT: B 254 MET cc_start: 0.5198 (mmp) cc_final: 0.4809 (mmp) REVERT: B 294 TYR cc_start: 0.7517 (m-80) cc_final: 0.7294 (m-80) outliers start: 23 outliers final: 13 residues processed: 117 average time/residue: 0.1020 time to fit residues: 15.9808 Evaluate side-chains 103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS 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 67 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 242 HIS 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: 9.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.171836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.156055 restraints weight = 74048.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.157909 restraints weight = 53859.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.158419 restraints weight = 40957.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.158530 restraints weight = 36227.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.159804 restraints weight = 35066.633| |-----------------------------------------------------------------------------| r_work (final): 0.4601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9738 Z= 0.124 Angle : 0.604 11.431 13953 Z= 0.307 Chirality : 0.035 0.382 1674 Planarity : 0.005 0.050 1157 Dihedral : 21.464 104.323 3364 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.40 % Allowed : 18.45 % 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: -1.13 (0.32), residues: 694 helix: 0.33 (0.28), residues: 390 sheet: -2.24 (0.80), residues: 42 loop : -2.13 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 72 TYR 0.018 0.002 TYR A 123 PHE 0.028 0.002 PHE B 35 TRP 0.006 0.001 TRP B 98 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9738) covalent geometry : angle 0.60425 / 0.31 (13953) hydrogen bonds : bond 0.04842 / 3.26 ( 392) hydrogen bonds : angle 4.40280 / 3.03 ( 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 119 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.185 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: A 64 TYR cc_start: 0.7594 (p90) cc_final: 0.7345 (p90) REVERT: A 133 MET cc_start: 0.4918 (OUTLIER) cc_final: 0.4057 (mmm) REVERT: A 165 GLN cc_start: 0.8913 (mm110) cc_final: 0.8713 (mm-40) REVERT: A 166 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8595 (ttmt) REVERT: A 265 MET cc_start: 0.8593 (mmm) cc_final: 0.8120 (mmm) REVERT: A 269 GLU cc_start: 0.9123 (tt0) cc_final: 0.8720 (tm-30) REVERT: B 86 ASN cc_start: 0.8995 (m110) cc_final: 0.8627 (p0) REVERT: B 110 MET cc_start: 0.6323 (ptp) cc_final: 0.4780 (pmm) REVERT: B 113 ASP cc_start: 0.9141 (p0) cc_final: 0.8535 (p0) REVERT: B 116 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8788 (mtpt) REVERT: B 133 MET cc_start: 0.5288 (ptm) cc_final: 0.4948 (ptt) REVERT: B 179 MET cc_start: 0.6094 (ttt) cc_final: 0.4157 (tpt) REVERT: B 228 ASP cc_start: 0.8339 (m-30) cc_final: 0.8035 (m-30) REVERT: B 229 ASP cc_start: 0.8297 (m-30) cc_final: 0.8018 (m-30) REVERT: B 254 MET cc_start: 0.5307 (OUTLIER) cc_final: 0.4749 (mmp) REVERT: B 294 TYR cc_start: 0.7427 (m-10) cc_final: 0.7177 (m-80) outliers start: 21 outliers final: 13 residues processed: 114 average time/residue: 0.1021 time to fit residues: 15.8078 Evaluate side-chains 106 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN A 241 HIS ** A 273 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.155922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.138849 restraints weight = 75222.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.141088 restraints weight = 57730.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.141486 restraints weight = 41852.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.141371 restraints weight = 38285.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.141795 restraints weight = 37966.831| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9738 Z= 0.297 Angle : 0.868 25.508 13953 Z= 0.449 Chirality : 0.045 0.485 1674 Planarity : 0.006 0.055 1157 Dihedral : 22.052 109.733 3364 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 38.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.53 % Allowed : 17.48 % Favored : 77.99 % 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: -2.08 (0.30), residues: 694 helix: -0.65 (0.26), residues: 388 sheet: -2.53 (0.77), residues: 46 loop : -2.17 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 39 TYR 0.021 0.003 TYR B 64 PHE 0.028 0.004 PHE B 204 TRP 0.017 0.003 TRP B 302 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.30 ( 9738) covalent geometry : angle 0.86818 / 0.45 (13953) hydrogen bonds : bond 0.11333 / 7.62 ( 392) hydrogen bonds : angle 5.23590 / 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 123 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5072 (mmt) REVERT: A 166 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.8791 (ttmm) REVERT: A 179 MET cc_start: 0.5657 (tpp) cc_final: 0.5313 (tpp) REVERT: A 265 MET cc_start: 0.8962 (mmm) cc_final: 0.8758 (mmm) REVERT: A 346 LYS cc_start: 0.9415 (tppt) cc_final: 0.9068 (tptp) REVERT: B 73 MET cc_start: 0.5521 (ppp) cc_final: 0.5153 (ppp) REVERT: B 110 MET cc_start: 0.7696 (ptp) cc_final: 0.7122 (ptp) REVERT: B 113 ASP cc_start: 0.9272 (p0) cc_final: 0.8755 (p0) REVERT: B 133 MET cc_start: 0.6159 (ptm) cc_final: 0.5569 (ptm) REVERT: B 214 MET cc_start: 0.6922 (pmm) cc_final: 0.6445 (mmm) REVERT: B 228 ASP cc_start: 0.8729 (m-30) cc_final: 0.8347 (m-30) REVERT: B 229 ASP cc_start: 0.8705 (m-30) cc_final: 0.8446 (m-30) REVERT: B 254 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5643 (mmp) REVERT: B 294 TYR cc_start: 0.7663 (m-10) cc_final: 0.7214 (m-80) outliers start: 28 outliers final: 22 residues processed: 113 average time/residue: 0.0992 time to fit residues: 15.2184 Evaluate side-chains 116 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 35 PHE Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 194 TYR 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 304 ASN Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 313 ASP 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: 10.0000 chunk 17 optimal weight: 0.0030 chunk 79 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.164267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.148339 restraints weight = 73221.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.149294 restraints weight = 54744.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.150451 restraints weight = 44066.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.150441 restraints weight = 37007.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.150941 restraints weight = 36587.451| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9738 Z= 0.146 Angle : 0.678 15.065 13953 Z= 0.351 Chirality : 0.039 0.395 1674 Planarity : 0.005 0.039 1157 Dihedral : 21.927 101.848 3364 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.07 % Allowed : 21.68 % Favored : 75.24 % 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: -1.56 (0.31), residues: 694 helix: -0.16 (0.27), residues: 390 sheet: -2.31 (0.84), residues: 42 loop : -2.08 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 94 TYR 0.027 0.003 TYR B 297 PHE 0.029 0.003 PHE B 35 TRP 0.010 0.002 TRP A 157 HIS 0.008 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 9738) covalent geometry : angle 0.67778 / 0.35 (13953) hydrogen bonds : bond 0.05966 / 3.98 ( 392) hydrogen bonds : angle 4.80868 / 3.29 ( 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 109 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.265 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: A 129 LYS cc_start: 0.9218 (tttt) cc_final: 0.8851 (tppt) REVERT: A 133 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.3787 (mmm) REVERT: A 243 MET cc_start: 0.8986 (pmm) cc_final: 0.8477 (mpp) REVERT: A 251 GLN cc_start: 0.4073 (OUTLIER) cc_final: 0.2273 (pp30) REVERT: A 265 MET cc_start: 0.8752 (mmm) cc_final: 0.8382 (mmm) REVERT: B 58 LYS cc_start: 0.5179 (OUTLIER) cc_final: 0.4730 (pttp) REVERT: B 214 MET cc_start: 0.6669 (pmm) cc_final: 0.6272 (mmm) REVERT: B 228 ASP cc_start: 0.8569 (m-30) cc_final: 0.8164 (m-30) REVERT: B 229 ASP cc_start: 0.8482 (m-30) cc_final: 0.8180 (m-30) REVERT: B 254 MET cc_start: 0.5771 (OUTLIER) cc_final: 0.5312 (mmp) REVERT: B 294 TYR cc_start: 0.7522 (m-10) cc_final: 0.7239 (m-80) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 0.1057 time to fit residues: 14.8945 Evaluate side-chains 103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 214 MET Chi-restraints excluded: chain A residue 251 GLN 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 67 PHE 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 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: 2.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 chunk 27 optimal weight: 0.7980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 251 GLN ** 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 = 0.4910 r_free = 0.4910 target = 0.164371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.148053 restraints weight = 73798.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.149323 restraints weight = 54933.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.150229 restraints weight = 44334.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.150231 restraints weight = 38680.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.150732 restraints weight = 37747.187| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9738 Z= 0.141 Angle : 0.661 15.268 13953 Z= 0.342 Chirality : 0.038 0.353 1674 Planarity : 0.005 0.057 1157 Dihedral : 21.833 102.541 3364 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.27 % Allowed : 22.98 % Favored : 74.76 % 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: -1.37 (0.32), residues: 694 helix: -0.04 (0.27), residues: 390 sheet: -2.00 (0.88), residues: 42 loop : -1.98 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 94 TYR 0.031 0.003 TYR A 64 PHE 0.033 0.003 PHE B 35 TRP 0.013 0.001 TRP A 157 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9738) covalent geometry : angle 0.66147 / 0.34 (13953) hydrogen bonds : bond 0.05445 / 3.63 ( 392) hydrogen bonds : angle 4.78092 / 3.25 ( 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 108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.313 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 129 LYS cc_start: 0.9229 (tttt) cc_final: 0.8861 (tppt) REVERT: A 133 MET cc_start: 0.5431 (mmp) cc_final: 0.3770 (mmm) REVERT: A 243 MET cc_start: 0.8984 (pmm) cc_final: 0.8468 (mpp) REVERT: A 265 MET cc_start: 0.8655 (mmm) cc_final: 0.8158 (mmm) REVERT: A 346 LYS cc_start: 0.9375 (tppt) cc_final: 0.9009 (tptp) REVERT: B 58 LYS cc_start: 0.5013 (OUTLIER) cc_final: 0.4542 (pttp) REVERT: B 177 GLN cc_start: 0.7430 (pm20) cc_final: 0.6565 (mm-40) REVERT: B 179 MET cc_start: 0.7093 (ttt) cc_final: 0.5096 (tpp) REVERT: B 214 MET cc_start: 0.6997 (pmm) cc_final: 0.6630 (mmm) REVERT: B 228 ASP cc_start: 0.8572 (m-30) cc_final: 0.8262 (m-30) REVERT: B 229 ASP cc_start: 0.8490 (m-30) cc_final: 0.8220 (m-30) REVERT: B 254 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.5118 (mmp) REVERT: B 294 TYR cc_start: 0.7412 (m-10) cc_final: 0.7075 (m-80) outliers start: 14 outliers final: 12 residues processed: 104 average time/residue: 0.0957 time to fit residues: 13.7502 Evaluate side-chains 104 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 214 MET 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 67 PHE 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 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: 0.9980 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 251 GLN ** 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 = 0.4917 r_free = 0.4917 target = 0.164833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.148863 restraints weight = 73440.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.149931 restraints weight = 55328.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.150914 restraints weight = 44159.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.150977 restraints weight = 37374.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.151645 restraints weight = 36650.497| |-----------------------------------------------------------------------------| r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9738 Z= 0.136 Angle : 0.686 18.938 13953 Z= 0.344 Chirality : 0.037 0.349 1674 Planarity : 0.005 0.091 1157 Dihedral : 21.758 102.634 3364 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.91 % Allowed : 22.98 % 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: -1.28 (0.32), residues: 694 helix: 0.02 (0.27), residues: 392 sheet: -1.96 (0.89), residues: 42 loop : -1.93 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 39 TYR 0.028 0.003 TYR A 64 PHE 0.036 0.003 PHE B 35 TRP 0.014 0.002 TRP A 157 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 9738) covalent geometry : angle 0.68568 / 0.34 (13953) hydrogen bonds : bond 0.05301 / 3.52 ( 392) hydrogen bonds : angle 4.72444 / 3.24 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1676.33 seconds wall clock time: 29 minutes 38.52 seconds (1778.52 seconds total)