Starting phenix.real_space_refine on Sun Apr 5 03:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9om0_70602/04_2026/9om0_70602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9om0_70602/04_2026/9om0_70602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9om0_70602/04_2026/9om0_70602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9om0_70602/04_2026/9om0_70602.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9om0_70602/04_2026/9om0_70602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9om0_70602/04_2026/9om0_70602.map" } resolution = 2.58 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= 0.001 sd= 0.017 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 9 5.49 5 S 39 5.16 5 C 4983 2.51 5 N 1281 2.21 5 O 1479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7791 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2524 Classifications: {'peptide': 323} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 307} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C Time building chain proxies: 1.45, per 1000 atoms: 0.19 Number of scatterers: 7791 At special positions: 0 Unit cell: (88.992, 84.872, 124.424, 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 39 16.00 P 9 15.00 O 1479 8.00 N 1281 7.00 C 4983 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.02 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.02 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 133 " " NAG A 503 " - " ASN A 310 " " NAG A 504 " - " ASN A 194 " " NAG B 502 " - " ASN B 133 " " NAG B 503 " - " ASN B 310 " " NAG B 504 " - " ASN B 194 " " NAG C 502 " - " ASN C 133 " " NAG C 503 " - " ASN C 310 " " NAG C 504 " - " ASN C 194 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 280.9 milliseconds 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 30.1% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.539A pdb=" N TYR A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.596A pdb=" N CYS A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.508A pdb=" N LYS A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 337 through 363 Processing helix chain 'B' and resid 42 through 64 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.539A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.595A pdb=" N CYS B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.508A pdb=" N LYS B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 337 through 363 Processing helix chain 'C' and resid 42 through 64 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.539A pdb=" N TYR C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 98' Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.596A pdb=" N CYS C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.508A pdb=" N LYS C 224 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 337 through 363 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 72 current: chain 'A' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 126 current: chain 'A' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 282 through 287 current: chain 'A' and resid 312 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 72 current: chain 'B' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 107 through 126 current: chain 'B' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 282 through 287 current: chain 'B' and resid 312 through 336 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 83 Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 72 current: chain 'C' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 126 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 282 through 287 current: chain 'C' and resid 312 through 336 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 83 Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88 229 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.89 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: 2421 1.34 - 1.46: 1892 1.46 - 1.58: 3619 1.58 - 1.69: 15 1.69 - 1.81: 45 Bond restraints: 7992 Sorted by residual: bond pdb=" C VAL A 95 " pdb=" N GLU A 96 " ideal model delta sigma weight residual 1.335 1.290 0.044 1.38e-02 5.25e+03 1.04e+01 bond pdb=" C VAL C 95 " pdb=" N GLU C 96 " ideal model delta sigma weight residual 1.335 1.291 0.044 1.38e-02 5.25e+03 1.02e+01 bond pdb=" C VAL B 95 " pdb=" N GLU B 96 " ideal model delta sigma weight residual 1.335 1.291 0.044 1.38e-02 5.25e+03 1.00e+01 bond pdb=" N TYR C 306 " pdb=" CA TYR C 306 " ideal model delta sigma weight residual 1.455 1.479 -0.023 1.22e-02 6.72e+03 3.59e+00 bond pdb=" N TYR B 306 " pdb=" CA TYR B 306 " ideal model delta sigma weight residual 1.455 1.479 -0.023 1.22e-02 6.72e+03 3.59e+00 ... (remaining 7987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 10544 1.37 - 2.75: 280 2.75 - 4.12: 36 4.12 - 5.50: 6 5.50 - 6.87: 12 Bond angle restraints: 10878 Sorted by residual: angle pdb=" N TYR C 306 " pdb=" CA TYR C 306 " pdb=" CB TYR C 306 " ideal model delta sigma weight residual 110.52 103.78 6.74 1.65e+00 3.67e-01 1.67e+01 angle pdb=" N TYR B 306 " pdb=" CA TYR B 306 " pdb=" CB TYR B 306 " ideal model delta sigma weight residual 110.52 103.79 6.73 1.65e+00 3.67e-01 1.66e+01 angle pdb=" N TYR A 306 " pdb=" CA TYR A 306 " pdb=" CB TYR A 306 " ideal model delta sigma weight residual 110.52 103.81 6.71 1.65e+00 3.67e-01 1.65e+01 angle pdb=" CB GLU A 96 " pdb=" CG GLU A 96 " pdb=" CD GLU A 96 " ideal model delta sigma weight residual 112.60 119.47 -6.87 1.70e+00 3.46e-01 1.63e+01 angle pdb=" CB GLU B 96 " pdb=" CG GLU B 96 " pdb=" CD GLU B 96 " ideal model delta sigma weight residual 112.60 119.46 -6.86 1.70e+00 3.46e-01 1.63e+01 ... (remaining 10873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 4494 15.65 - 31.30: 246 31.30 - 46.94: 90 46.94 - 62.59: 39 62.59 - 78.24: 9 Dihedral angle restraints: 4878 sinusoidal: 2097 harmonic: 2781 Sorted by residual: dihedral pdb=" CA MET C 191 " pdb=" CB MET C 191 " pdb=" CG MET C 191 " pdb=" SD MET C 191 " ideal model delta sinusoidal sigma weight residual 180.00 128.28 51.72 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA MET A 191 " pdb=" CB MET A 191 " pdb=" CG MET A 191 " pdb=" SD MET A 191 " ideal model delta sinusoidal sigma weight residual 180.00 128.31 51.69 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA MET B 191 " pdb=" CB MET B 191 " pdb=" CG MET B 191 " pdb=" SD MET B 191 " ideal model delta sinusoidal sigma weight residual 180.00 128.32 51.68 3 1.50e+01 4.44e-03 9.04e+00 ... (remaining 4875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 824 0.040 - 0.079: 280 0.079 - 0.119: 122 0.119 - 0.159: 10 0.159 - 0.198: 3 Chirality restraints: 1239 Sorted by residual: chirality pdb=" CA ASN C 310 " pdb=" N ASN C 310 " pdb=" C ASN C 310 " pdb=" CB ASN C 310 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA ASN B 310 " pdb=" N ASN B 310 " pdb=" C ASN B 310 " pdb=" CB ASN B 310 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CA ASN A 310 " pdb=" N ASN A 310 " pdb=" C ASN A 310 " pdb=" CB ASN A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1236 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 305 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" C LYS A 305 " 0.020 2.00e-02 2.50e+03 pdb=" O LYS A 305 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR A 306 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 280 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO B 281 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 305 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C LYS B 305 " -0.020 2.00e-02 2.50e+03 pdb=" O LYS B 305 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR B 306 " 0.007 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1663 2.79 - 3.32: 6959 3.32 - 3.84: 12844 3.84 - 4.37: 15270 4.37 - 4.90: 26336 Nonbonded interactions: 63072 Sorted by model distance: nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.261 3.040 nonbonded pdb=" O GLY C 84 " pdb=" OH TYR C 98 " model vdw 2.261 3.040 nonbonded pdb=" O GLY B 84 " pdb=" OH TYR B 98 " model vdw 2.261 3.040 nonbonded pdb=" O GLU A 103 " pdb=" OH TYR B 299 " model vdw 2.371 3.040 nonbonded pdb=" O GLU B 103 " pdb=" OH TYR C 299 " model vdw 2.373 3.040 ... (remaining 63067 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.780 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.004 0.044 8016 Z= 0.201 Angle : 0.605 9.978 10935 Z= 0.321 Chirality : 0.047 0.198 1239 Planarity : 0.004 0.029 1344 Dihedral : 12.324 78.240 3063 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.17 % Allowed : 6.14 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 963 helix: 0.52 (0.34), residues: 228 sheet: 0.72 (0.26), residues: 354 loop : -1.02 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.013 0.001 TYR C 321 PHE 0.007 0.001 PHE B 239 TRP 0.011 0.001 TRP A 268 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 7992) covalent geometry : angle 0.56816 (10878) SS BOND : bond 0.00359 ( 15) SS BOND : angle 1.01805 ( 30) hydrogen bonds : bond 0.16225 ( 229) hydrogen bonds : angle 6.83243 ( 597) link_NAG-ASN : bond 0.00497 ( 9) link_NAG-ASN : angle 4.10994 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.293 Fit side-chains REVERT: A 75 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7214 (mt-10) REVERT: A 233 ASP cc_start: 0.8259 (m-30) cc_final: 0.8047 (m-30) REVERT: A 250 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7316 (mm-30) REVERT: B 87 THR cc_start: 0.8688 (p) cc_final: 0.8484 (t) REVERT: B 127 GLU cc_start: 0.7764 (tp30) cc_final: 0.7465 (tp30) REVERT: B 224 LYS cc_start: 0.8357 (mtpp) cc_final: 0.8142 (mtpp) REVERT: B 286 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7522 (ttm110) REVERT: C 103 GLU cc_start: 0.7705 (mp0) cc_final: 0.7295 (mp0) REVERT: C 270 CYS cc_start: 0.7669 (m) cc_final: 0.7460 (m) REVERT: C 280 ASN cc_start: 0.8237 (m-40) cc_final: 0.7945 (m-40) outliers start: 18 outliers final: 14 residues processed: 242 average time/residue: 0.6000 time to fit residues: 152.5081 Evaluate side-chains 221 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 152 ASN B 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110568 restraints weight = 10896.946| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.91 r_work: 0.3409 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8016 Z= 0.200 Angle : 0.616 11.547 10935 Z= 0.302 Chirality : 0.050 0.203 1239 Planarity : 0.004 0.030 1344 Dihedral : 10.670 62.949 1357 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.73 % Allowed : 12.03 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 963 helix: 0.51 (0.33), residues: 231 sheet: 0.70 (0.26), residues: 348 loop : -0.99 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 130 TYR 0.016 0.002 TYR B 98 PHE 0.015 0.002 PHE A 56 TRP 0.020 0.001 TRP B 268 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 7992) covalent geometry : angle 0.56377 (10878) SS BOND : bond 0.00510 ( 15) SS BOND : angle 1.03878 ( 30) hydrogen bonds : bond 0.04241 ( 229) hydrogen bonds : angle 5.46144 ( 597) link_NAG-ASN : bond 0.00549 ( 9) link_NAG-ASN : angle 4.94636 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.305 Fit side-chains REVERT: A 75 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7465 (mt-10) REVERT: A 220 ASP cc_start: 0.7191 (t0) cc_final: 0.6976 (t0) REVERT: A 227 THR cc_start: 0.8050 (t) cc_final: 0.7819 (m) REVERT: A 250 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 258 LYS cc_start: 0.8092 (tppt) cc_final: 0.7748 (mppt) REVERT: B 188 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8158 (mt) REVERT: B 224 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8303 (mtpp) REVERT: B 258 LYS cc_start: 0.8150 (tppt) cc_final: 0.7930 (tppt) REVERT: B 286 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7787 (ttm170) REVERT: C 122 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8703 (mm110) REVERT: C 191 MET cc_start: 0.7687 (mpp) cc_final: 0.7397 (mmm) REVERT: C 250 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7561 (mm-30) REVERT: C 280 ASN cc_start: 0.8326 (m-40) cc_final: 0.8058 (m-40) outliers start: 31 outliers final: 20 residues processed: 228 average time/residue: 0.5767 time to fit residues: 138.3748 Evaluate side-chains 223 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 292 HIS C 201 ASN C 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.124497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108967 restraints weight = 10879.970| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.93 r_work: 0.3402 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 8016 Z= 0.313 Angle : 0.677 11.999 10935 Z= 0.335 Chirality : 0.053 0.224 1239 Planarity : 0.005 0.045 1344 Dihedral : 10.668 67.787 1357 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 5.54 % Allowed : 13.96 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 963 helix: -0.09 (0.31), residues: 231 sheet: 0.61 (0.26), residues: 348 loop : -1.17 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.019 0.002 TYR B 98 PHE 0.017 0.002 PHE A 56 TRP 0.024 0.002 TRP B 268 HIS 0.004 0.001 HIS C 229 Details of bonding type rmsd covalent geometry : bond 0.00773 ( 7992) covalent geometry : angle 0.62466 (10878) SS BOND : bond 0.00634 ( 15) SS BOND : angle 1.42662 ( 30) hydrogen bonds : bond 0.04593 ( 229) hydrogen bonds : angle 5.62930 ( 597) link_NAG-ASN : bond 0.00414 ( 9) link_NAG-ASN : angle 5.09771 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.283 Fit side-chains REVERT: A 220 ASP cc_start: 0.7449 (t0) cc_final: 0.7038 (t0) REVERT: A 227 THR cc_start: 0.8057 (t) cc_final: 0.7795 (m) REVERT: A 250 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 258 LYS cc_start: 0.8138 (tppt) cc_final: 0.7793 (mppt) REVERT: B 224 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8338 (mtpp) REVERT: B 324 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: C 103 GLU cc_start: 0.7919 (mp0) cc_final: 0.7360 (mp0) REVERT: C 191 MET cc_start: 0.7727 (mpp) cc_final: 0.7450 (mmm) REVERT: C 250 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 280 ASN cc_start: 0.8399 (m-40) cc_final: 0.8116 (m-40) outliers start: 46 outliers final: 31 residues processed: 230 average time/residue: 0.5747 time to fit residues: 138.9987 Evaluate side-chains 230 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 51 optimal weight: 0.0370 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 67 optimal weight: 0.0050 chunk 27 optimal weight: 0.9980 overall best weight: 0.3250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS C 122 GLN C 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111165 restraints weight = 11066.651| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.94 r_work: 0.3427 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8016 Z= 0.115 Angle : 0.588 11.512 10935 Z= 0.283 Chirality : 0.048 0.191 1239 Planarity : 0.004 0.033 1344 Dihedral : 10.025 64.130 1357 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.85 % Allowed : 17.33 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 963 helix: 0.70 (0.34), residues: 231 sheet: 0.72 (0.27), residues: 348 loop : -0.98 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 130 TYR 0.015 0.001 TYR B 321 PHE 0.016 0.001 PHE A 56 TRP 0.013 0.001 TRP B 268 HIS 0.001 0.000 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7992) covalent geometry : angle 0.53662 (10878) SS BOND : bond 0.00327 ( 15) SS BOND : angle 0.87889 ( 30) hydrogen bonds : bond 0.03445 ( 229) hydrogen bonds : angle 5.18459 ( 597) link_NAG-ASN : bond 0.00661 ( 9) link_NAG-ASN : angle 4.83248 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.216 Fit side-chains REVERT: A 220 ASP cc_start: 0.7356 (t0) cc_final: 0.7067 (t0) REVERT: A 225 ARG cc_start: 0.8194 (ptt180) cc_final: 0.7985 (ptt180) REVERT: A 233 ASP cc_start: 0.8351 (m-30) cc_final: 0.8139 (m-30) REVERT: A 250 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7553 (mm-30) REVERT: A 258 LYS cc_start: 0.8110 (tppt) cc_final: 0.7765 (mppt) REVERT: B 258 LYS cc_start: 0.8134 (tppt) cc_final: 0.7910 (tppt) REVERT: B 286 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.7833 (ttm170) REVERT: C 152 ASN cc_start: 0.8507 (m-40) cc_final: 0.8288 (m110) REVERT: C 191 MET cc_start: 0.7792 (mpp) cc_final: 0.7442 (mmm) REVERT: C 250 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7595 (mm-30) REVERT: C 280 ASN cc_start: 0.8259 (m-40) cc_final: 0.7993 (m-40) outliers start: 32 outliers final: 24 residues processed: 221 average time/residue: 0.5838 time to fit residues: 135.7477 Evaluate side-chains 223 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 17 optimal weight: 0.0770 chunk 34 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.0370 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111667 restraints weight = 11068.172| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.92 r_work: 0.3433 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8016 Z= 0.115 Angle : 0.568 11.232 10935 Z= 0.276 Chirality : 0.047 0.196 1239 Planarity : 0.004 0.032 1344 Dihedral : 9.723 65.763 1357 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.49 % Allowed : 18.05 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 963 helix: 1.07 (0.34), residues: 231 sheet: 0.75 (0.27), residues: 348 loop : -0.91 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.015 0.001 TYR B 321 PHE 0.017 0.001 PHE B 56 TRP 0.010 0.001 TRP B 268 HIS 0.001 0.000 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7992) covalent geometry : angle 0.51665 (10878) SS BOND : bond 0.00322 ( 15) SS BOND : angle 0.92754 ( 30) hydrogen bonds : bond 0.03266 ( 229) hydrogen bonds : angle 5.01900 ( 597) link_NAG-ASN : bond 0.00629 ( 9) link_NAG-ASN : angle 4.69945 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.278 Fit side-chains REVERT: A 75 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7454 (mt-10) REVERT: A 220 ASP cc_start: 0.7278 (t0) cc_final: 0.6944 (t0) REVERT: A 225 ARG cc_start: 0.8187 (ptt180) cc_final: 0.7961 (ptt180) REVERT: A 227 THR cc_start: 0.8057 (t) cc_final: 0.7740 (m) REVERT: A 233 ASP cc_start: 0.8348 (m-30) cc_final: 0.8142 (m-30) REVERT: A 250 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 258 LYS cc_start: 0.8111 (tppt) cc_final: 0.7770 (mppt) REVERT: B 224 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8190 (mtpp) REVERT: B 258 LYS cc_start: 0.8133 (tppt) cc_final: 0.7863 (tppt) REVERT: B 286 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.7873 (ttm170) REVERT: B 324 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7644 (ttm170) REVERT: C 191 MET cc_start: 0.7795 (mpp) cc_final: 0.7443 (mmm) REVERT: C 250 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7581 (mm-30) REVERT: C 280 ASN cc_start: 0.8248 (m-40) cc_final: 0.7988 (m-40) outliers start: 29 outliers final: 24 residues processed: 218 average time/residue: 0.5750 time to fit residues: 132.0764 Evaluate side-chains 220 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 122 GLN C 152 ASN C 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110537 restraints weight = 10964.477| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.92 r_work: 0.3424 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8016 Z= 0.193 Angle : 0.603 11.209 10935 Z= 0.296 Chirality : 0.050 0.219 1239 Planarity : 0.004 0.033 1344 Dihedral : 9.836 66.771 1357 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.81 % Allowed : 17.45 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 963 helix: 0.77 (0.33), residues: 231 sheet: 0.76 (0.27), residues: 348 loop : -0.96 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.017 0.002 TYR B 321 PHE 0.016 0.001 PHE A 56 TRP 0.016 0.001 TRP B 268 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 7992) covalent geometry : angle 0.55369 (10878) SS BOND : bond 0.00492 ( 15) SS BOND : angle 1.24089 ( 30) hydrogen bonds : bond 0.03630 ( 229) hydrogen bonds : angle 5.18790 ( 597) link_NAG-ASN : bond 0.00501 ( 9) link_NAG-ASN : angle 4.71906 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.289 Fit side-chains REVERT: A 220 ASP cc_start: 0.7258 (t0) cc_final: 0.6790 (t0) REVERT: A 224 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7903 (mtpp) REVERT: A 227 THR cc_start: 0.8041 (t) cc_final: 0.7779 (m) REVERT: A 250 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 258 LYS cc_start: 0.8122 (tppt) cc_final: 0.7776 (mppt) REVERT: B 127 GLU cc_start: 0.7859 (tp30) cc_final: 0.7633 (tp30) REVERT: B 191 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7251 (mtm) REVERT: B 258 LYS cc_start: 0.8140 (tppt) cc_final: 0.7919 (tppt) REVERT: B 286 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7854 (ttm170) REVERT: B 324 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7661 (ttm170) REVERT: C 188 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8051 (mt) REVERT: C 191 MET cc_start: 0.7798 (mpp) cc_final: 0.7457 (mmm) REVERT: C 250 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7607 (mm-30) outliers start: 40 outliers final: 29 residues processed: 218 average time/residue: 0.5757 time to fit residues: 132.2118 Evaluate side-chains 226 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 152 ASN C 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111198 restraints weight = 10898.719| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.92 r_work: 0.3429 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8016 Z= 0.127 Angle : 0.592 11.895 10935 Z= 0.285 Chirality : 0.048 0.216 1239 Planarity : 0.004 0.030 1344 Dihedral : 9.744 69.865 1357 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.61 % Allowed : 19.01 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 963 helix: 1.05 (0.34), residues: 231 sheet: 0.77 (0.27), residues: 348 loop : -0.91 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.016 0.001 TYR B 321 PHE 0.017 0.001 PHE A 56 TRP 0.013 0.001 TRP B 268 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7992) covalent geometry : angle 0.54360 (10878) SS BOND : bond 0.00402 ( 15) SS BOND : angle 1.07130 ( 30) hydrogen bonds : bond 0.03260 ( 229) hydrogen bonds : angle 5.06193 ( 597) link_NAG-ASN : bond 0.00604 ( 9) link_NAG-ASN : angle 4.63234 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 201 ASN cc_start: 0.8697 (t0) cc_final: 0.8488 (t0) REVERT: A 220 ASP cc_start: 0.7190 (t0) cc_final: 0.6870 (t0) REVERT: A 224 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7875 (mtpp) REVERT: A 225 ARG cc_start: 0.8168 (ptt180) cc_final: 0.7910 (ptt180) REVERT: A 250 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 258 LYS cc_start: 0.8118 (tppt) cc_final: 0.7769 (mppt) REVERT: B 127 GLU cc_start: 0.7873 (tp30) cc_final: 0.7643 (tp30) REVERT: B 152 ASN cc_start: 0.8604 (m-40) cc_final: 0.8361 (m110) REVERT: B 191 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7245 (mtm) REVERT: B 258 LYS cc_start: 0.8104 (tppt) cc_final: 0.7889 (tppt) REVERT: B 324 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7652 (ttm170) REVERT: C 191 MET cc_start: 0.7812 (mpp) cc_final: 0.7473 (mmm) REVERT: C 250 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7595 (mm-30) outliers start: 30 outliers final: 26 residues processed: 217 average time/residue: 0.5751 time to fit residues: 131.2500 Evaluate side-chains 224 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 152 ASN C 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111054 restraints weight = 10977.686| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.93 r_work: 0.3414 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8016 Z= 0.149 Angle : 0.595 11.421 10935 Z= 0.288 Chirality : 0.049 0.230 1239 Planarity : 0.004 0.029 1344 Dihedral : 9.736 69.426 1357 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.97 % Allowed : 18.89 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 963 helix: 1.02 (0.34), residues: 231 sheet: 0.78 (0.27), residues: 348 loop : -0.90 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.017 0.001 TYR B 321 PHE 0.007 0.001 PHE A 252 TRP 0.014 0.001 TRP B 268 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7992) covalent geometry : angle 0.54846 (10878) SS BOND : bond 0.00445 ( 15) SS BOND : angle 1.13392 ( 30) hydrogen bonds : bond 0.03348 ( 229) hydrogen bonds : angle 5.07625 ( 597) link_NAG-ASN : bond 0.00552 ( 9) link_NAG-ASN : angle 4.57847 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 220 ASP cc_start: 0.7137 (t0) cc_final: 0.6684 (t0) REVERT: A 250 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 258 LYS cc_start: 0.8111 (tppt) cc_final: 0.7764 (mppt) REVERT: B 127 GLU cc_start: 0.7888 (tp30) cc_final: 0.7651 (tp30) REVERT: B 191 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7209 (mtm) REVERT: B 258 LYS cc_start: 0.8096 (tppt) cc_final: 0.7879 (tppt) REVERT: B 324 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7649 (ttm170) REVERT: C 188 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8045 (mt) REVERT: C 191 MET cc_start: 0.7812 (mpp) cc_final: 0.7477 (mmm) REVERT: C 250 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7609 (mm-30) outliers start: 33 outliers final: 29 residues processed: 218 average time/residue: 0.5785 time to fit residues: 132.8239 Evaluate side-chains 231 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 0.0370 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 9 optimal weight: 0.0060 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN C 122 GLN C 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.127566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111938 restraints weight = 11021.958| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.94 r_work: 0.3429 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8016 Z= 0.114 Angle : 0.576 11.213 10935 Z= 0.278 Chirality : 0.048 0.228 1239 Planarity : 0.004 0.027 1344 Dihedral : 9.587 68.096 1357 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.73 % Allowed : 19.86 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 963 helix: 1.87 (0.36), residues: 213 sheet: 0.82 (0.27), residues: 348 loop : -0.73 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.015 0.001 TYR B 321 PHE 0.018 0.001 PHE C 56 TRP 0.012 0.001 TRP C 268 HIS 0.002 0.000 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7992) covalent geometry : angle 0.53028 (10878) SS BOND : bond 0.00343 ( 15) SS BOND : angle 1.01494 ( 30) hydrogen bonds : bond 0.03073 ( 229) hydrogen bonds : angle 4.93208 ( 597) link_NAG-ASN : bond 0.00620 ( 9) link_NAG-ASN : angle 4.48460 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 258 LYS cc_start: 0.8105 (tppt) cc_final: 0.7756 (mppt) REVERT: B 127 GLU cc_start: 0.7880 (tp30) cc_final: 0.7656 (tp30) REVERT: B 152 ASN cc_start: 0.8601 (m-40) cc_final: 0.8365 (m110) REVERT: B 191 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7278 (mtm) REVERT: B 258 LYS cc_start: 0.8107 (tppt) cc_final: 0.7845 (tppt) REVERT: B 308 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8818 (mmtm) REVERT: B 324 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7643 (ttm170) REVERT: C 188 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8042 (mt) REVERT: C 191 MET cc_start: 0.7824 (mpp) cc_final: 0.7480 (mmm) REVERT: C 250 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7613 (mm-30) outliers start: 31 outliers final: 25 residues processed: 216 average time/residue: 0.5666 time to fit residues: 128.8735 Evaluate side-chains 224 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.126541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.110924 restraints weight = 10953.246| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.93 r_work: 0.3426 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8016 Z= 0.176 Angle : 0.611 11.119 10935 Z= 0.298 Chirality : 0.050 0.265 1239 Planarity : 0.004 0.029 1344 Dihedral : 9.688 68.897 1356 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.37 % Allowed : 20.58 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 963 helix: 1.02 (0.34), residues: 231 sheet: 0.87 (0.27), residues: 345 loop : -0.86 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.018 0.001 TYR B 321 PHE 0.018 0.001 PHE A 56 TRP 0.014 0.001 TRP B 268 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7992) covalent geometry : angle 0.56590 (10878) SS BOND : bond 0.00502 ( 15) SS BOND : angle 1.26237 ( 30) hydrogen bonds : bond 0.03432 ( 229) hydrogen bonds : angle 5.08983 ( 597) link_NAG-ASN : bond 0.00503 ( 9) link_NAG-ASN : angle 4.50004 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.252 Fit side-chains REVERT: A 227 THR cc_start: 0.8029 (t) cc_final: 0.7803 (p) REVERT: A 250 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 258 LYS cc_start: 0.8126 (tppt) cc_final: 0.7779 (mppt) REVERT: B 127 GLU cc_start: 0.7866 (tp30) cc_final: 0.7659 (tp30) REVERT: B 152 ASN cc_start: 0.8611 (m-40) cc_final: 0.8390 (m110) REVERT: B 191 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7279 (mtm) REVERT: B 258 LYS cc_start: 0.8123 (tppt) cc_final: 0.7899 (tppt) REVERT: B 286 ARG cc_start: 0.8233 (ttp-110) cc_final: 0.7842 (ttm170) REVERT: B 324 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7646 (ttm170) REVERT: C 188 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8069 (mt) REVERT: C 191 MET cc_start: 0.7811 (mpp) cc_final: 0.7489 (mmm) REVERT: C 250 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7635 (mm-30) outliers start: 28 outliers final: 25 residues processed: 211 average time/residue: 0.5903 time to fit residues: 131.0198 Evaluate side-chains 222 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 357 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 201 ASN C 122 GLN C 152 ASN C 201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111168 restraints weight = 10880.442| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.92 r_work: 0.3428 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 8016 Z= 0.207 Angle : 0.970 58.949 10935 Z= 0.566 Chirality : 0.055 0.904 1239 Planarity : 0.004 0.042 1344 Dihedral : 9.720 68.893 1356 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.49 % Allowed : 20.82 % Favored : 75.69 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.26), residues: 963 helix: 1.02 (0.34), residues: 231 sheet: 0.87 (0.27), residues: 345 loop : -0.86 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.016 0.001 TYR B 321 PHE 0.016 0.001 PHE A 56 TRP 0.014 0.001 TRP B 268 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 7992) covalent geometry : angle 0.94360 (10878) SS BOND : bond 0.00465 ( 15) SS BOND : angle 1.32476 ( 30) hydrogen bonds : bond 0.03411 ( 229) hydrogen bonds : angle 5.08961 ( 597) link_NAG-ASN : bond 0.00503 ( 9) link_NAG-ASN : angle 4.50091 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3642.02 seconds wall clock time: 62 minutes 31.98 seconds (3751.98 seconds total)